1TGV | pdb_00001tgv

Structure of E. coli Uridine Phosphorylase complexed with 5-Fluorouridine and sulfate

PDB DOI: https://doi.org/10.2210/pdb1TGV/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2004-05-31 Released: 2005-06-14
Deposition Author(s): Bu, W., Settembre, E.C., Sanders, J.M., Begley, T.P., Ealick, S.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.224 (Depositor), 0.216 (DCC)
R-Value Work:
0.175 (Depositor), 0.167 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structures of E. coli Uridine Phosphorylase

Bu, W., Settembre, E.C., Sanders, J.M., Begley, T.P., Ealick, S.E.

To be published.

Macromolecule Content

Total Structure Weight: 55.7 kDa
Atom Count: 3,983
Modeled Residue Count: 492
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uridine phosphorylase	A, B	256	Escherichia coli	Mutation(s): 0 Gene Names: UDP, B3831 EC: 2.4.2.3
UniProt
Find proteins for P12758 (Escherichia coli (strain K12)) Explore P12758 Go to UniProtKB: P12758
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12758
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5UD Query on 5UD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	5-FLUOROURIDINE C₉ H₁₁ F N₂ O₆ FHIDNBAQOFJWCA-UAKXSSHOSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.224 (Depositor), 0.216 (DCC)
R-Value Work: 0.175 (Depositor), 0.167 (DCC)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.972	α = 90
b = 149.972	β = 90
c = 49.566	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-06-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-06-14
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations

1TGV | pdb_00001tgv

Structure of E. coli Uridine Phosphorylase complexed with 5-Fluorouridine and sulfate

Literature

Structures of E. coli Uridine Phosphorylase

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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