3VE9 | pdb_00003ve9

Crystal structure of orotidine 5'-monophosphate decarboxylase from Metallosphaera sedula

• PDB DOI: https://doi.org/10.2210/pdb3VE9/pdb

• Classification: LYASE
• Organism(s): Metallosphaera sedula DSM 5348
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-07 Released: 2013-01-09 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.214 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of orotidine 5'-monophosphate decarboxylase from Metallosphaera sedula

Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.07 kDa 
• Atom Count: 3,539 
• Modeled Residue Count: 408 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine-5'-phosphate decarboxylase	A, B	215	Metallosphaera sedula DSM 5348	Mutation(s): 0  Gene Names: Msed_1966 EC: 4.1.1.23
UniProt
Find proteins for A4YI54 (Metallosphaera sedula (strain ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2)) Explore A4YI54  Go to UniProtKB:  A4YI54

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.214 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.097	α = 90
b = 74.87	β = 95.54
c = 55.097	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description