4NX5 | pdb_00004nx5

Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

• PDB DOI: https://doi.org/10.2210/pdb4NX5/pdb

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


• Deposited: 2013-12-08 Released: 2013-12-25 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Chan, K.K., Gerlt, J.A., Almo, S.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

Fedorov, A.A., Fedorov, E.V., Chan, K.K., 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: 50.86 kDa 
• Atom Count: 3,951 
• Modeled Residue Count: 439 
• 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UP6	C [auth A], G [auth B]	6-AZA URIDINE 5'-MONOPHOSPHATE C8 H12 N3 O9 P LRVZOSYMNMNQFR-SHUUEZRQSA-N
GOL	J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A], E [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	L [auth B], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UP6	BindingDB:  4NX5	Ki: 1.24e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.737	α = 90
b = 64.148	β = 115.36
c = 61.527	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Chan, K.K., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description