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)

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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) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable hemolysin	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	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

Entry History 

Deposition Data

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

Revision History  

• 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