3VXB | pdb_00003vxb

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 (Depositor), 0.240 (DCC)
R-Value Work:
0.190 (Depositor), 0.188 (DCC)
R-Value Observed:
0.192 (Depositor)

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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
Modeled Residue Count: 399
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [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 (Depositor), 0.240 (DCC)
R-Value Work: 0.190 (Depositor), 0.188 (DCC)
R-Value Observed: 0.192 (Depositor)

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

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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

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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.