5TVG | pdb_00005tvg

Crystal structure of an alpha,alpha-trehalose-phosphate synthase (UDP-forming) from Burkholderia vietnamiensis

PDB DOI: https://doi.org/10.2210/pdb5TVG/pdb

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

Deposited: 2016-11-08 Released: 2016-11-16
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:
0.225 (Depositor), 0.230 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of an alpha,alpha-trehalose-phosphate synthase (UDP-forming) from Burkholderia vietnamiensis

Edwards, T.E., Conrady, D.G., Fairman, J.W., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 435.38 kDa
Atom Count: 28,914
Modeled Residue Count: 3,621
Deposited Residue Count: 3,848
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha,alpha-trehalose-phosphate synthase (UDP-forming)	A, B, C, D, E A, B, C, D, E, F, G, H	481	Burkholderia vietnamiensis G4	Mutation(s): 0 Gene Names: Bcep1808_2483 EC: 2.4.1.15
UniProt
Find proteins for A4JGS8 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JGS8 Go to UniProtKB: A4JGS8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4JGS8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain CA [auth G] SDF format, chain EA [auth H] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth E]	AA [auth F] CA [auth G] EA [auth H] I [auth A] P [auth B] AA [auth F], CA [auth G], EA [auth H], I [auth A], P [auth B], S [auth C], U [auth D], Y [auth E]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain Y [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain DA [auth G] SDF format, chain FA [auth H] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E]	BA [auth F] DA [auth G] FA [auth H] J [auth A] K [auth A] BA [auth F], DA [auth G], FA [auth H], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], Q [auth B], T [auth C], V [auth D], W [auth D], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain X [auth D] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain X [auth D] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain X [auth D]	O [auth A], R [auth B], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain R [auth B] Focus chain X [auth D] Interactions & Density Focus chain O [auth A] Focus chain R [auth B] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.225 (Depositor), 0.230 (DCC)
R-Value Work: 0.178 (Depositor), 0.180 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.17	α = 90
b = 103.02	β = 96.42
c = 218.47	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
BALBES	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-11-16

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-11-16
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description