5KLX

Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110

PDB DOI: https://doi.org/10.2210/pdb5KLX/pdb

Classification: ISOMERASE, protein binding
Organism(s): Saccharomyces cerevisiae S288C, Burkholderia pseudomallei 1710b
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-06-26 Released: 2017-05-31
Deposition Author(s): Fox III, D., Edwards, T.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.256
R-Value Work: 0.198
R-Value Observed: 0.201

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110

Lorimer, D.D., Fox III, D., Seufert, F., Edwards, T.E., Holzgrabe, U.

To be published.

Macromolecule Content

Total Structure Weight: 94.03 kDa
Atom Count: 5,458
Modelled Residue Count: 734
Deposited Residue Count: 836
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase	A, B, C, D	209	Saccharomyces cerevisiae S288C, Burkholderia pseudomallei 1710b This entity is chimeric	Mutation(s): 0 Gene Names: SMT3, YDR510W, D9719.15, BURPS1710b_A0907 EC: 5.2.1.8
UniProt
Find proteins for Q3JK38 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JK38 Go to UniProtKB: Q3JK38
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306 Go to UniProtKB: Q12306
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q3JK38Q12306
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6UO Query on 6UO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D]	E [auth A], I [auth B], J [auth C], K [auth D]	2-[(2~{S})-1-(phenylmethyl)sulfonylpiperidin-2-yl]carbonyloxyethyl pyridine-3-carboxylate C₂₁ H₂₄ N₂ O₆ S KUWLHSSIHRTCQU-IBGZPJMESA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth D] mmCIF format, chain G [auth A] mmCIF format, chain M [auth D]	G [auth A], M [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain M [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth D]	F [auth A], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.256
R-Value Work: 0.198
R-Value Observed: 0.201
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.89	α = 90
b = 34.11	β = 115.45
c = 119.92	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-05-31

Deposition Author(s):

Fox III, D.

Edwards, T.E.

Revision History (Full details and data files)

Version 1.0: 2017-05-31
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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5KLX

Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110

Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)