4DF1 | pdb_00004df1

Crystal structure of orotidine 5'-monophosphate decarboxylase from Thermoproteus neutrophilus complexed with inhibitor BMP

• PDB DOI: https://doi.org/10.2210/pdb4DF1/pdb

• Classification: LYASE/LYASE inhibitor
• Organism(s): Pyrobaculum neutrophilum V24Sta
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-22 Released: 2013-01-23 
• 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: 1.90 Å
• R-Value Free: 
  0.179 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of orotidine 5'-monophosphate decarboxylase from Thermoproteus neutrophilus complexed with inhibitor BMP

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: 44.7 kDa 
• Atom Count: 3,437 
• Modeled Residue Count: 398 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	202	Pyrobaculum neutrophilum V24Sta	Mutation(s): 0  Gene Names: Tneu_0023 EC: 4.1.1.23
UniProt
Find proteins for B1Y9Q9 (Pyrobaculum neutrophilum (strain DSM 2338 / JCM 9278 / NBRC 100436 / V24Sta)) Explore B1Y9Q9  Go to UniProtKB:  B1Y9Q9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMP	C [auth A], E [auth B]	6-HYDROXYURIDINE-5'-PHOSPHATE C9 H13 N2 O10 P UDOBICLZEKUKCV-YXZULKJRSA-N
NI	D [auth A], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.179 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.158	α = 90
b = 62.071	β = 97.46
c = 72.712	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: 2013-01-23 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary