3VE7 | pdb_00003ve7

Crystal structure of orotidine 5'-monophosphate decarboxylase from Metallosphaera sedula complexed with inhibitor BMP

PDB DOI: https://doi.org/10.2210/pdb3VE7/pdb

Classification: LYASE/LYASE INHIBITOR
Organism(s): Metallosphaera sedula DSM 5348
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-01-07 Released: 2013-01-09
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: 1.54 Å
R-Value Free:
0.201 (Depositor), 0.198 (DCC)
R-Value Work:
0.169 (Depositor), 0.164 (DCC)
R-Value Observed:
0.170 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of orotidine 5'-monophosphate decarboxylase from Metallosphaera sedula complexed with inhibitor BMP

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

To be published.

Macromolecule Content

Total Structure Weight: 48.02 kDa
Atom Count: 3,569
Modeled Residue Count: 411
Deposited Residue Count: 430
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	215	Metallosphaera sedula DSM 5348	Mutation(s): 0 Gene Names: Msed_1966 EC: 4.1.1.23
UniProt
Find proteins for A4YI54 (Metallosphaera sedula (strain ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2)) Explore A4YI54 Go to UniProtKB: A4YI54
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4YI54
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BMP Query on BMP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	6-HYDROXYURIDINE-5'-PHOSPHATE C₉ H₁₃ N₂ O₁₀ P UDOBICLZEKUKCV-YXZULKJRSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B], G [auth B], H [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.201 (Depositor), 0.198 (DCC)
R-Value Work: 0.169 (Depositor), 0.164 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.396	α = 90
b = 91.57	β = 98.79
c = 50.954	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-01-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-01-09
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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