4QB5 | pdb_00004qb5

Crystal structure of a glyoxalase/bleomycin resistance protein from Albidiferax ferrireducens T118

• PDB DOI: https://doi.org/10.2210/pdb4QB5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodoferax ferrireducens T118
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-06 Released: 2014-07-23 
• Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.211 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of a glyoxalase/bleomycin resistance protein from Albidiferax ferrireducens T118

Kumaran, D., Almo, S.C., Swaminathan, S.

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 (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 (software)

Macromolecule Content 

• Total Structure Weight: 64.08 kDa 
• Atom Count: 3,897 
• Modeled Residue Count: 490 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A, B, C, D	148	Rhodoferax ferrireducens T118	Mutation(s): 0  Gene Names: Rfer_4015
UniProt
Find proteins for Q21R90 (Albidiferax ferrireducens (strain ATCC BAA-621 / DSM 15236 / T118)) Explore Q21R90  Go to UniProtKB:  Q21R90

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B], F [auth D], G [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	H [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 2.05 Å
• R-Value Free:  0.211 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.949	α = 90
b = 89.896	β = 90
c = 131.857	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary