5VE7 | pdb_00005ve7

Crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia ambifaria in complex with UTP

PDB DOI: https://doi.org/10.2210/pdb5VE7/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia ambifaria MC40-6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-04-04 Released: 2017-04-12
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.221 (Depositor), 0.213 (DCC)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.182 (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 UTP-glucose-1-phosphate uridylyltransferase from Burkholderia ambifaria in complex with UTP

Abendroth, J., Higgins, T.W., Dranow, D.M., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 33.78 kDa
Atom Count: 2,384
Modeled Residue Count: 282
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UTP--glucose-1-phosphate uridylyltransferase	A	302	Burkholderia ambifaria MC40-6	Mutation(s): 0 Gene Names: BamMC406_1359 EC: 2.7.7.9
UniProt
Find proteins for B1YNX3 (Burkholderia ambifaria (strain MC40-6)) Explore B1YNX3 Go to UniProtKB: B1YNX3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1YNX3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UTP Query on UTP 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]	URIDINE 5'-TRIPHOSPHATE C₉ H₁₅ N₂ O₁₅ P₃ PGAVKCOVUIYSFO-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.221 (Depositor), 0.213 (DCC)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.182 (Depositor)

Diffraction Data:

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.25	α = 90
b = 108.48	β = 90
c = 124.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-04-12

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-04-12
Type: Initial release
Version 1.1: 2017-12-13
Changes: Advisory
Version 1.2: 2023-10-04
Changes: Data collection, Database references, 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.