3VPM | pdb_00003vpm

Crystal structure of human ribonucleotide reductase subunit M2 (hRRM2) mutant

• PDB DOI: https://doi.org/10.2210/pdb3VPM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-03-05 Released: 2013-03-06 
• Deposition Author(s): Chen, X., Xu, Z., Liu, H., Zhang, L., Chen, B., Zhu, L., Yang, C., Zhu, W., Shao, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.249 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Essential role of E106 in the proton-coupled electron transfer in human ribonucleotide reductase M2 subunit

Chen, X., Xu, Z., Liu, H., Zhang, L., Chen, B., Zhu, L., Yang, C., Zhu, W., Shao, J.

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)

Macromolecule Content 

• Total Structure Weight: 67.28 kDa 
• Atom Count: 4,786 
• Modeled Residue Count: 572 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase subunit M2	A, B	286	Homo sapiens	Mutation(s): 1  Gene Names: RR2, RRM2 EC: 1.17.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for P31350 (Homo sapiens) Explore P31350  Go to UniProtKB:  P31350
PHAROS:  P31350 GTEx:  ENSG00000171848

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	D [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.249 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.998	α = 90
b = 108.998	β = 90
c = 174.948	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Chen, X., Xu, Z., Liu, H., Zhang, L., Chen, B., Zhu, L., Yang, C., Zhu, W., Shao, J.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description