4WML | pdb_00004wml

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

• PDB DOI: https://doi.org/10.2210/pdb4WML/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-09 Released: 2015-12-23 
• Deposition Author(s): Bang, M.B., Molich, U., Hansen, M.R., Grubmeyer, C., Harris, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.250 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.77 kDa 
• Atom Count: 1,852 
• Modeled Residue Count: 216 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotate phosphoribosyltransferase 1	A	231	Saccharomyces cerevisiae S288C	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPC	C [auth A]	1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose C6 H15 O13 P3 JFMKBQDEISBIPL-KVTDHHQDSA-N
MG	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 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.56	α = 90
b = 61.56	β = 90
c = 132.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Bang, M.B., Molich, U., Hansen, M.R., Grubmeyer, C., Harris, P.

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