3VXB

Crystal Structure of BxlE from Streptomyces thermoviolaceus OPC-520

PDB DOI: https://doi.org/10.2210/pdb3VXB/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Streptomyces thermoviolaceus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-11 Released: 2013-09-18
Deposition Author(s): Tomoo, K., Ishida, T., Miyamoto, K., Tsujibo, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.240
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Xylooligosaccharide-Binding Protein from Streptomyces thermoviolaceus OPC-520: Dramatic Conformational Change with Ligand binding

Tomoo, K., Ishida, T., Miyamoto, K., Tsujibo, H.

To be published.

Macromolecule Content

Total Structure Weight: 47.08 kDa
Atom Count: 3,148
Modelled Residue Count: 399
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sugar-binding lipoprotein	A	436	Streptomyces thermoviolaceus	Mutation(s): 0 Gene Names: bxlD
UniProt
Find proteins for Q76BU9 (Streptomyces thermoviolaceus) Explore Q76BU9 Go to UniProtKB: Q76BU9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q76BU9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.240
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.634	α = 90
b = 63.272	β = 103.05
c = 66.402	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
SOLVE	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.