3DED | pdb_00003ded

C-terminal domain of Probable hemolysin from Chromobacterium violaceum

PDB DOI: https://doi.org/10.2210/pdb3DED/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Chromobacterium violaceum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-09 Released: 2008-08-05
Deposition Author(s): Chang, C., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.235 (Depositor), 0.230 (DCC)
R-Value Work:
0.186 (Depositor), 0.182 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of C-terminal domain of Probable hemolysin from Chromobacterium violaceum

Chang, C., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 79.76 kDa
Atom Count: 4,716
Modelled Residue Count: 523
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable hemolysin	A, B, C, D, E A, B, C, D, E, F	113	Chromobacterium violaceum	Mutation(s): 0 Gene Names: CV_0231
UniProt
Find proteins for Q7P1I2 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7P1I2 Go to UniProtKB: Q7P1I2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7P1I2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth E] mmCIF format, chain O [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	G [auth A] H [auth A] I [auth B] J [auth C] K [auth C] G [auth A], H [auth A], I [auth B], J [auth C], K [auth C], L [auth D], M [auth E], N [auth E], O [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.235 (Depositor), 0.230 (DCC)
R-Value Work: 0.186 (Depositor), 0.182 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.144	α = 90
b = 55.312	β = 94.34
c = 93.734	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-05

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Derived calculations, Refinement description, Version format compliance
Version 1.2: 2018-01-31
Changes: Database references
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

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C-terminal domain of Probable hemolysin from Chromobacterium violaceum

Crystal structure of C-terminal domain of Probable hemolysin from Chromobacterium violaceum

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

3DED | pdb_00003ded