4NT0 | pdb_00004nt0

Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 3-deazauridine 5'-monophosphate

• PDB DOI: https://doi.org/10.2210/pdb4NT0/pdb

• Classification: LYASE
• Organism(s): Methanothermobacter thermautotrophicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-11-29 Released: 2013-12-18 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Iiams, V., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.227 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 3-deazauridine 5'-monophosphate

Fedorov, A.A., Fedorov, E.V., Iiams, V., 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: 50.6 kDa 
• Atom Count: 3,538 
• Modeled Residue Count: 426 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	228	Methanothermobacter thermautotrophicus	Mutation(s): 1  Gene Names: pyrF, MTH_129 EC: 4.1.1.23
UniProt
Find proteins for O26232 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26232  Go to UniProtKB:  O26232

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3DU	C [auth A], F [auth B]	4-hydroxy-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-2(1H)-one C10 H14 N O9 P BMAAJONJGSMHCR-PEBGCTIMSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.227 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.886	α = 90
b = 56.896	β = 90
c = 125.179	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-18 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Iiams, V., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description