3VPN | pdb_00003vpn

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

• PDB DOI: https://doi.org/10.2210/pdb3VPN/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: 2.25 Å
• R-Value Free: 
  0.247 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Essential role of E106 in the proton-coupled electron transfer in human

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: 67.37 kDa 
• Atom Count: 4,960 
• 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	C [auth A], E [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.247 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.082	α = 90
b = 109.082	β = 90
c = 176.523	γ = 90

Software Package:

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

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