4N2Y | pdb_00004n2y

Crystal structure of orotidine 5'-monophosphate decarboxylase from Archaeoglobus fulgidus

PDB DOI: https://doi.org/10.2210/pdb4N2Y/pdb

Classification: LYASE
Organism(s): Archaeoglobus fulgidus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-10-06 Released: 2013-10-30
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.209 (Depositor), 0.208 (DCC)
R-Value Work:
0.184 (Depositor), 0.185 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of orotidine 5'-monophosphate decarboxylase from Archaeoglobus fulgidus

Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 99.06 kDa
Atom Count: 6,790
Modeled Residue Count: 813
Deposited Residue Count: 916
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B, C, D	229	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: pyrF, AF_0929 EC: 4.1.1.23
UniProt
Find proteins for O29333 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29333 Go to UniProtKB: O29333
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O29333
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.209 (Depositor), 0.208 (DCC)
R-Value Work: 0.184 (Depositor), 0.185 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.563	α = 90
b = 116.859	β = 90.12
c = 87.147	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-30
Type: Initial release
Version 1.1: 2013-11-06
Changes: Database references, Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-27
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.