4WML

Crystal structure of Saccharomyces cerevisiae OMP synthase in complex with PRP(CH2)P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of Saccharomyces cerevisia OMP synthase in complex with PRP(CH2)P

Bang, M.B.Molich, U.Hansen, M.R.Grubmeyer, C.Harris, P.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Orotate phosphoribosyltransferase 1A231Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: URA5PYR5YML106WYM8339.13
EC: 2.4.2.10
Find proteins for P13298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13298 
Go to UniProtKB:  P13298
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PPC
Query on PPC

Download Ideal Coordinates CCD File 
A
1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose
C6 H15 O13 P3
JFMKBQDEISBIPL-KVTDHHQDSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.56α = 90
b = 61.56β = 90
c = 132.49γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Data collection
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary