3SGU | pdb_00003sgu

Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase covalently modified by 5-fluoro-6-iodo-UMP

• PDB DOI: https://doi.org/10.2210/pdb3SGU/pdb

• Classification: LYASE
• Organism(s): Methanothermobacter thermautotrophicus str. Delta H
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-15 Released: 2012-05-02 
• Deposition Author(s): Liu, Y., Kotra, L.P., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase covalently modified by 5-fluoro-6-iodo-UMP

Liu, Y., Kotra, L.P., Pai, E.F.

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: 27.17 kDa 
• Atom Count: 1,868 
• Modeled Residue Count: 213 
• Deposited Residue Count: 247 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A	247	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0  Gene Names: 1470090, MTH_129, pyrF 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5FU	B [auth A]	5-FLUORO-URIDINE-5'-MONOPHOSPHATE C9 H12 F N2 O9 P RNBMPPYRHNWTMA-UAKXSSHOSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
5FU	BindingDB:  3SGU	Ki: 6.45e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.891	α = 90
b = 103.709	β = 90
c = 73.68	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Liu, Y., Kotra, L.P., Pai, E.F.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Structure summary
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary