2EAW | pdb_00002eaw

Human UMP Synthase (C-terminal Domain- Orotidine 5'-Monophosphate Decarboxylase)

PDB DOI: https://doi.org/10.2210/pdb2EAW/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-02-03 Released: 2007-02-13
Deposition Author(s): Liu, Y., Tang, H.L., Pai, E.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.307 (Depositor), 0.297 (DCC)
R-Value Work:
0.259 (Depositor), 0.258 (DCC)
R-Value Observed:
0.262 (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

Human UMP Synthase (C-terminal Domain - Orotidine 5'-Monophosphate Decarboxylase)

Liu, Y., Tang, H.L., Pai, E.F.

To be published.

Macromolecule Content

Total Structure Weight: 63.6 kDa
Atom Count: 3,925
Modeled Residue Count: 512
Deposited Residue Count: 582
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine 5'-monophosphate synthase	A, B	291	Homo sapiens	Mutation(s): 0 Gene Names: UMPS EC: 4.1.1.23 (PDB Primary Data), 2.4.2.10 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P11172 (Homo sapiens) Explore P11172 Go to UniProtKB: P11172
PHAROS: P11172 GTEx: ENSG00000114491
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11172
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.307 (Depositor), 0.297 (DCC)
R-Value Work: 0.259 (Depositor), 0.258 (DCC)
R-Value Observed: 0.262 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.571	α = 90
b = 59.37	β = 114.3
c = 69.863	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data collection
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-02-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-02-13
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.