4IQ0 | pdb_00004iq0

Crystal structure of oxidoreductase, Gfo/Idh/MocA family from Streptococcus pneumoniae with reductive methylated Lysine

• PDB DOI: https://doi.org/10.2210/pdb4IQ0/pdb
• Entry: 4IQ0 supersedes: 2HO3

• Classification: OXIDOREDUCTASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-10 Released: 2013-01-23 
• Deposition Author(s): Chang, C., Hatzos-Skintges, C., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.195 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Literature

Crystal structure of oxidoreductase, Gfo/Idh/MocA family from Streptococcus pneumoniae with reductive methylated Lysine

Chang, C., Hatzos-Skintges, C., Abdullah, J., 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: 148.27 kDa 
• Atom Count: 10,806 
• Modeled Residue Count: 1,231 
• Deposited Residue Count: 1,312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, Gfo/Idh/MocA family	A, B, C, D	328	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: SP_1482
UniProt
Find proteins for A0A0H2UR04 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UR04  Go to UniProtKB:  A0A0H2UR04

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	E [auth B], F [auth B], G [auth C], H [auth D], I [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B, C, D	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.195 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34IQ0

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.915	α = 90
b = 152.386	β = 103.12
c = 100.237	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Chang, C., Hatzos-Skintges, C., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 2HO3

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary