4HC5 | pdb_00004hc5

Crystal structure of member of Glyoxalase/bleomycin resistance protein/dioxygenase superfamily from Sphaerobacter thermophilus DSM 20745

• PDB DOI: https://doi.org/10.2210/pdb4HC5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sphaerobacter thermophilus DSM 20745
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-28 Released: 2012-11-28 
• Deposition Author(s): Nocek, B., Hatzos-Skintges, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.145 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Crystal structure of member of Glyoxalase/bleomycin resistance protein/dioxygenase superfamily from Sphaerobacter thermophilus DSM 20745

Nocek, B., Hatzos-Skintges, C., Jedrzejczak, R., 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 (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: 61.01 kDa 
• Atom Count: 4,620 
• Modeled Residue Count: 508 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A, B, C, D	133	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0  Gene Names: Sthe_2956
UniProt
Find proteins for D1C967 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C967  Go to UniProtKB:  D1C967

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.45 Å
• R-Value Free:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.145 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34HC5

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.883	α = 90
b = 71.023	β = 90
c = 86.698	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELX	model building
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-28 
Deposition Author(s): Nocek, B., Hatzos-Skintges, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-11-28
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary