3SW6 | pdb_00003sw6

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

PDB DOI: https://doi.org/10.2210/pdb3SW6/pdb

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

Deposited: 2011-07-13 Released: 2012-05-02
Deposition Author(s): Liu, Y., Kotra, L.P., Pai, E.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.189 (Depositor), 0.191 (DCC)
R-Value Work:
0.161 (Depositor), 0.161 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

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

Liu, Y., Kotra, L.P., Pai, E.F.

To be published.

Macromolecule Content

Total Structure Weight: 27.14 kDa
Atom Count: 1,992
Modeled Residue Count: 214
Deposited Residue Count: 247
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26232
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5FU Query on 5FU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	5-FLUORO-URIDINE-5'-MONOPHOSPHATE C₉ H₁₂ F N₂ O₉ P RNBMPPYRHNWTMA-UAKXSSHOSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.189 (Depositor), 0.191 (DCC)
R-Value Work: 0.161 (Depositor), 0.161 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.118	α = 90
b = 103.37	β = 90
c = 73.92	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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-05-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.