3QC3 | pdb_00003qc3

Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954699) from HOMO SAPIENS at 2.20 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.211 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3QC3

This is version 1.5 of the entry. See complete history. 

Literature

Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954699) from HOMO SAPIENS at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content 

  • Total Structure Weight: 51.03 kDa 
  • Atom Count: 3,705 
  • Modeled Residue Count: 450 
  • Deposited Residue Count: 450 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
D-ribulose-5-phosphate-3-epimerase
A, B
225Homo sapiensMutation(s): 0 
Gene Names: RPE, HUSSY-17
EC: 5.1.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96AT9 (Homo sapiens)
Explore Q96AT9 
Go to UniProtKB:  Q96AT9
PHAROS:  Q96AT9
GTEx:  ENSG00000197713 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96AT9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL


Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI

Query on NI


Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]		NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
FE

Query on FE


Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]		FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.211 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.665α = 90
b = 47.665β = 90
c = 220.774γ = 90
Software Package:
Software NamePurpose
SHELXphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-20
    Changes: Structure summary
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-10-09
    Changes: Data collection, Refinement description, Structure summary