5IFY | pdb_00005ify

Crystal structure of Glucose-1-phosphate thymidylyltransferase from Burkholderia vietnamiensis in complex with 2 -Deoxyuridine-5'-monophosphate and 2'-Deoxy-Thymidine-B-L-Rhamnose

PDB DOI: https://doi.org/10.2210/pdb5IFY/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia vietnamiensis G4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-02-26 Released: 2016-03-09
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.197 (Depositor), 0.199 (DCC)
R-Value Work:
0.157 (Depositor), 0.160 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Glucose-1-phosphate thymidylyltransferase from Burkholderia vietnamiensis in complex with 2'-Deoxyuridine-5'-monophosphate and 2'-Deoxy-Thymidine-B-L-Rhamnose

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

To be published.

Macromolecule Content

Total Structure Weight: 209.54 kDa
Atom Count: 14,509
Modeled Residue Count: 1,753
Deposited Residue Count: 1,830
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate thymidylyltransferase	A, B, C, D, E A, B, C, D, E, F	305	Burkholderia vietnamiensis G4	Mutation(s): 0 Gene Names: Bcep1808_0806 EC: 2.7.7.24
UniProt
Find proteins for A4JC15 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JC15 Go to UniProtKB: A4JC15
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4JC15
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRH Query on TRH Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain Q [auth F] SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE C₁₆ H₂₆ N₂ O₁₅ P₂ ZOSQFDVXNQFKBY-CGAXJHMRSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]
UMP Query on UMP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth C] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain N [auth D] SDF format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth C] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain N [auth D] MOL2 format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth C] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain N [auth D] mmCIF format, chain J [auth B]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.197 (Depositor), 0.199 (DCC)
R-Value Work: 0.157 (Depositor), 0.160 (DCC)
R-Value Observed: 0.158 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.6	α = 90
b = 254.72	β = 90
c = 82.05	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

5IFY | pdb_00005ify

Crystal structure of Glucose-1-phosphate thymidylyltransferase from Burkholderia vietnamiensis in complex with 2 -Deoxyuridine-5'-monophosphate and 2'-Deoxy-Thymidine-B-L-Rhamnose

Literature

Crystal structure of Glucose-1-phosphate thymidylyltransferase from Burkholderia vietnamiensis in complex with 2'-Deoxyuridine-5'-monophosphate and 2'-Deoxy-Thymidine-B-L-Rhamnose

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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