3TZH | pdb_00003tzh

Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(F187A) from Vibrio cholerae

PDB DOI: https://doi.org/10.2210/pdb3TZH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Vibrio cholerae MJ-1236
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-09-27 Released: 2011-10-19
Deposition Author(s): Hou, J., Chruszcz, M., Zheng, H., Cooper, D.R., Osinski, T., Shumilin, I., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.191 (Depositor), 0.200 (DCC)
R-Value Work:
0.157 (Depositor), 0.170 (DCC)
R-Value Observed:
0.159 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 160.16 kDa
Atom Count: 11,881
Modelled Residue Count: 1,484
Deposited Residue Count: 1,506
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier protein] reductase	A, B, C, D, E A, B, C, D, E, F	251	Vibrio cholerae MJ-1236	Mutation(s): 1 Gene Names: VC2021, VCD_002346 EC: 1.1.1.100
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain BB [auth D] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain KB [auth E] SDF format, chain LB [auth E] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain WB [auth F] SDF format, chain XB [auth F] SDF format, chain YB [auth F] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain KB [auth E] MOL2 format, chain LB [auth E] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain WB [auth F] MOL2 format, chain XB [auth F] MOL2 format, chain YB [auth F] MOL2 format, chain ZA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain BB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain KB [auth E] mmCIF format, chain LB [auth E] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain WB [auth F] mmCIF format, chain XB [auth F] mmCIF format, chain YB [auth F] mmCIF format, chain ZA [auth D]	AB [auth D] BB [auth D] DA [auth B] EA [auth B] FA [auth B] AB [auth D], BB [auth D], DA [auth B], EA [auth B], FA [auth B], KB [auth E], LB [auth E], MA [auth C], NA [auth C], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], WB [auth F], XB [auth F], YB [auth F], ZA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth D] Focus chain BB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain WB [auth F] Focus chain XB [auth F] Focus chain YB [auth F] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain WB [auth F] Focus chain XB [auth F] Focus chain YB [auth F] Focus chain ZA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AC [auth F] SDF format, chain GA [auth B] SDF format, chain MB [auth E] SDF format, chain NB [auth E] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain ZB [auth F] MOL2 format, chain AC [auth F] MOL2 format, chain GA [auth B] MOL2 format, chain MB [auth E] MOL2 format, chain NB [auth E] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain ZB [auth F] mmCIF format, chain AC [auth F] mmCIF format, chain GA [auth B] mmCIF format, chain MB [auth E] mmCIF format, chain NB [auth E] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain ZB [auth F]	AC [auth F] GA [auth B] MB [auth E] NB [auth E] RA [auth C] AC [auth F], GA [auth B], MB [auth E], NB [auth E], RA [auth C], S [auth A], ZB [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AC [auth F] Focus chain GA [auth B] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain RA [auth C] Focus chain S [auth A] Focus chain ZB [auth F] Interactions & Density Focus chain AC [auth F] Focus chain GA [auth B] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain RA [auth C] Focus chain S [auth A] Focus chain ZB [auth F]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain CB [auth E] SDF format, chain DB [auth E] SDF format, chain EB [auth E] SDF format, chain FB [auth E] SDF format, chain G [auth A] SDF format, chain GB [auth E] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain HB [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain IB [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain JB [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OB [auth F] SDF format, chain PB [auth F] SDF format, chain QB [auth F] SDF format, chain RB [auth F] SDF format, chain SA [auth D] SDF format, chain SB [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain TB [auth F] SDF format, chain U [auth B] SDF format, chain UA [auth D] SDF format, chain UB [auth F] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain VB [auth F] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain FB [auth E] MOL2 format, chain G [auth A] MOL2 format, chain GB [auth E] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain JB [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth F] MOL2 format, chain PB [auth F] MOL2 format, chain QB [auth F] MOL2 format, chain RB [auth F] MOL2 format, chain SA [auth D] MOL2 format, chain SB [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain TB [auth F] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain UB [auth F] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain VB [auth F] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth E] mmCIF format, chain DB [auth E] mmCIF format, chain EB [auth E] mmCIF format, chain FB [auth E] mmCIF format, chain G [auth A] mmCIF format, chain GB [auth E] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain JB [auth E] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth F] mmCIF format, chain PB [auth F] mmCIF format, chain QB [auth F] mmCIF format, chain RB [auth F] mmCIF format, chain SA [auth D] mmCIF format, chain SB [auth F] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain TB [auth F] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain UB [auth F] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain VB [auth F] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] CB [auth E] DB [auth E] AA [auth B], BA [auth B], CA [auth B], CB [auth E], DB [auth E], EB [auth E], FB [auth E], G [auth A], GB [auth E], H [auth A], HA [auth C], HB [auth E], I [auth A], IA [auth C], IB [auth E], J [auth A], JA [auth C], JB [auth E], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], N [auth A], O [auth A], OB [auth F], PB [auth F], QB [auth F], RB [auth F], SA [auth D], SB [auth F], T [auth B], TA [auth D], TB [auth F], U [auth B], UA [auth D], UB [auth F], V [auth B], VA [auth D], VB [auth F], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain G [auth A] Focus chain GB [auth E] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth E] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OB [auth F] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SA [auth D] Focus chain SB [auth F] Focus chain T [auth B] Focus chain TA [auth D] Focus chain TB [auth F] Focus chain U [auth B] Focus chain UA [auth D] Focus chain UB [auth F] Focus chain V [auth B] Focus chain VA [auth D] Focus chain VB [auth F] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain G [auth A] Focus chain GB [auth E] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth E] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OB [auth F] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SA [auth D] Focus chain SB [auth F] Focus chain T [auth B] Focus chain TA [auth D] Focus chain TB [auth F] Focus chain U [auth B] Focus chain UA [auth D] Focus chain UB [auth F] Focus chain V [auth B] Focus chain VA [auth D] Focus chain VB [auth F] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.191 (Depositor), 0.200 (DCC)
R-Value Work: 0.157 (Depositor), 0.170 (DCC)
R-Value Observed: 0.159 (Depositor)

Diffraction Data: https://doi.org/10.18430/m39w2f

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.341	α = 90
b = 380.354	β = 119.86
c = 63.212	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-10-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-10-19
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-02-28
Changes: Data collection