3KTB | pdb_00003ktb

Crystal Structure of Arsenical Resistance Operon Trans-acting Repressor from Bacteroides vulgatus ATCC 8482

• PDB DOI: https://doi.org/10.2210/pdb3KTB/pdb

• Classification: transcription regulator
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-11-24 Released: 2009-12-08 
• Deposition Author(s): Kim, Y., Tesar, C., Feldmann, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.219 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Crystal Structure of Arsenical Resistance Operon Trans-acting Repressor from Bacteroides vulgatus ATCC 8482

Kim, Y., Tesar, C., Feldmann, B., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 16-mer - A16 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 48.1 kDa 
• Atom Count: 3,783 
• Modeled Residue Count: 416 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arsenical resistance operon trans-acting repressor	A, B, C, D	106	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_4185
UniProt
Find proteins for A6L7X2 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L7X2  Go to UniProtKB:  A6L7X2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], H [auth C], J [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	F [auth B], G [auth C]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	I [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.219 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.911	α = 90
b = 115.911	β = 90
c = 83.579	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Kim, Y., Tesar, C., Feldmann, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary