3KOG | pdb_00003kog

Crystal structure of Putative pore-forming toxin (YP_001301288.1) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3KOG/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-13 Released: 2009-12-01 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.214 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of Putative pore-forming toxin (YP_001301288.1) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.37 kDa 
• Atom Count: 2,062 
• Modeled Residue Count: 226 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative pore-forming toxin	A	256	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_4064
UniProt
Find proteins for A6L7K2 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L7K2  Go to UniProtKB:  A6L7K2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	G [auth A], H [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	B [auth A], C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.214 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33KOG

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.796	α = 90
b = 70.337	β = 90
c = 104.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary