8B81 | pdb_00008b81

The structure of Gan1D W433A in complex with cellobiose-6-phosphate

PDB DOI: https://doi.org/10.2210/pdb8B81/pdb

Classification: HYDROLASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-10-04 Released: 2022-10-19
Deposition Author(s): Snyder, J., Lansky, S., Zehavi, A., Shoham, Y., Shoham, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.201 (Depositor), 0.206 (DCC)
R-Value Work:
0.169 (Depositor), 0.175 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The structure of Gan1D W433A in complex with cellobiose-6-phosphate

Snyder, J., Lansky, S., Zehavi, A., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 111.43 kDa
Atom Count: 8,977
Modeled Residue Count: 948
Deposited Residue Count: 956
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 6-phospho-beta-galactobiosidase	A, B	478	Geobacillus stearothermophilus	Mutation(s): 1 Gene Names: gan1D EC: 3.2.1.85
UniProt
Find proteins for W8QF82 (Geobacillus stearothermophilus) Explore W8QF82 Go to UniProtKB: W8QF82
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8QF82
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
6-O-phosphono-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C [auth E], D	2		N/A	Interactions Focus chain C [auth E] Focus chain D Interactions & Density Focus chain C [auth E] Focus chain D
Glycosylation Resources
GlyTouCan: G15380AW GlyCosmos: G15380AW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900053 Query on PRD_900053	C [auth D], D [auth E]	beta-cellobiose-6-phosphate	Oligosaccharide / Substrate analog		Interactions Focus chain C [auth E] Focus chain D Interactions & Density Focus chain C [auth E] Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.201 (Depositor), 0.206 (DCC)
R-Value Work: 0.169 (Depositor), 0.175 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.9	α = 90
b = 68.38	β = 99.36
c = 149.8	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	Israel	--

Revision History (Full details and data files)

Version 1.0: 2022-10-19
Type: Initial release
Version 1.1: 2024-01-31
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.