5C3M | pdb_00005c3m

Crystal structure of Gan4C, a GH4 6-phospho-glucosidase from Geobacillus stearothermophilus

PDB DOI: https://doi.org/10.2210/pdb5C3M/pdb

Classification: HYDROLASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-06-17 Released: 2016-06-29
Deposition Author(s): Cohen, T., Lansky, S., Zehavi, A., Shoham, Y., Shoham, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.06 Å
R-Value Free:
0.306 (Depositor), 0.307 (DCC)
R-Value Work:
0.230 (Depositor), 0.234 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Gan4C, a GH4 6-phospho-glucosidase from Geobacillus stearothermophilus

Cohen, T., Lansky, S., Zehavi, A., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 197.51 kDa
Atom Count: 12,494
Modeled Residue Count: 1,640
Deposited Residue Count: 1,788
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 6-phospho-beta-glucosidase	A, B, C, D	447	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: gan4C EC: 3.2.1.86
UniProt
Find proteins for W8R9V4 (Geobacillus stearothermophilus) Explore W8R9V4 Go to UniProtKB: W8R9V4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8R9V4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain H [auth D] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C]	E [auth A], F [auth B], G [auth C], H [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.06 Å
R-Value Free: 0.306 (Depositor), 0.307 (DCC)
R-Value Work: 0.230 (Depositor), 0.234 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.324	α = 90
b = 83.198	β = 113.61
c = 151.372	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, 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.