6GUQ | pdb_00006guq

Crystal structure of GanP, a glucose-galactose binding protein from Geobacillus stearothermophilus, in complex with glucose

PDB DOI: https://doi.org/10.2210/pdb6GUQ/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-06-19 Released: 2019-07-03
Deposition Author(s): Sherf, D., Lansky, S., Zehavi, A., Shoham, Y., Shoham, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.244 (Depositor), 0.247 (DCC)
R-Value Work:
0.198 (Depositor), 0.201 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6GUQ

Ligand Structure Quality Assessment

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

Literature

The crystal structure of GanP, a glucose-galactose binding protein from Geobacillus stearothermophilus, in complex with glucose

Sherf, D., Zehavi, A., Lansky, S., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 35.7 kDa
Atom Count: 2,248
Modeled Residue Count: 278
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sugar binding protein	A	318	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: ganP
UniProt
Find proteins for W8QN64 (Geobacillus stearothermophilus) Explore W8QN64 Go to UniProtKB: W8QN64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8QN64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC 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]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.244 (Depositor), 0.247 (DCC)
R-Value Work: 0.198 (Depositor), 0.201 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.97	α = 90
b = 70.97	β = 90
c = 149.19	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-07-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-07-03
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.