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 

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This is version 1.3 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orotate phosphoribosyltransferase 1231Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: URA5, PYR5, YML106W, YM8339.13
EC: 2.4.2.10
UniProt
Find proteins for P13298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13298 
Go to UniProtKB:  P13298
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13298
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PPC
Query on PPC
Download Ideal Coordinates CCD File 
C [auth A]1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose
C6 H15 O13 P3
JFMKBQDEISBIPL-KVTDHHQDSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary