5X3V | pdb_00005x3v

Structure of human SHMT2 protein mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5X3V

This is version 1.1 of the entry. See complete history

Literature

Structure of human SHMT2 protein mutant

Li, J.Sheng, J.

To be published.

Macromolecule Content 

  • Total Structure Weight: 110.74 kDa 
  • Atom Count: 6,984 
  • Modeled Residue Count: 887 
  • Deposited Residue Count: 992 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase, mitochondrial
A, B
496Homo sapiensMutation(s): 1 
Gene Names: SHMT2
EC: 2.1.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P34897 (Homo sapiens)
Explore P34897 
Go to UniProtKB:  P34897
PHAROS:  P34897
GTEx:  ENSG00000182199 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34897
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.655α = 90
b = 158.655β = 90
c = 209.358γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description