3C6Q | pdb_00003c6q

Apo and ligand-bound form of a thermophilic glucose/xylose binding protein

PDB DOI: https://doi.org/10.2210/pdb3C6Q/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2008-02-05 Released: 2008-02-26
Deposition Author(s): Cuneo, M.J., Hellinga, H.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.281 (Depositor), 0.233 (DCC)
R-Value Work:
0.214 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Open to closed transition of a thermophilic glucose binding protein

Cuneo, M.J., Hellinga, H.W.

To be published.

Macromolecule Content

Total Structure Weight: 135.13 kDa
Atom Count: 9,588
Modeled Residue Count: 1,220
Deposited Residue Count: 1,244
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter, periplasmic sugar-binding protein	A [auth B], B [auth A], C, D	311	Thermotoga maritima	Mutation(s): 2 Gene Names: TM0114
UniProt
Find proteins for Q9WXW9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXW9 Go to UniProtKB: Q9WXW9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WXW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XYP Query on XYP Download:Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain E [auth C] MOL2 format, chain F [auth D] MOL2 format, chain E [auth C] mmCIF format, chain F [auth D] mmCIF format, chain E [auth C]	E [auth C], F [auth D]	beta-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-KKQCNMDGSA-N		Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.281 (Depositor), 0.233 (DCC)
R-Value Work: 0.214 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.1	α = 90
b = 75.75	β = 89.9
c = 100.52	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-02-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-02-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2021-10-20
Changes: Database references, Structure summary
Version 2.2: 2023-08-30
Changes: Data collection, Refinement description

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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.