7VMA | pdb_00007vma

The X-ray crystallographic structure of amylo-alpha-1,6-glucosidase from Thermococcus gammatolerans STB12

PDB DOI: https://doi.org/10.2210/pdb7VMA/pdb

Classification: HYDROLASE
Organism(s): Thermococcus gammatolerans EJ3
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-10-08 Released: 2022-10-12
Deposition Author(s): Li, Z.F., Ban, X.F., Wang, Y.M., Li, C.M., Gu, Z.B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.328 (Depositor), 0.333 (DCC)
R-Value Work:
0.244 (Depositor), 0.251 (DCC)
R-Value Observed:
0.248 (Depositor)

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

Literature

The X-ray Crystallographic Structure of Amylo-alpha-1,6-glucosidase from Thermococcus gannatilerans STB12

Li, Z.F., Ban, X.F., Wang, Y.M., Li, C.M., Gu, Z.B.

To be published.

Macromolecule Content

Total Structure Weight: 137.41 kDa
Atom Count: 9,718
Modeled Residue Count: 1,240
Deposited Residue Count: 1,240
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amylo-alpha-1,6-glucosidase, putative archaeal type glycogen debranching enzyme (Gde)	A, B	620	Thermococcus gammatolerans EJ3	Mutation(s): 0 Gene Names: gde, TGAM_1568 EC: 3.2.1.33
UniProt
Find proteins for C5A758 (Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3)) Explore C5A758 Go to UniProtKB: C5A758
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C5A758
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.328 (Depositor), 0.333 (DCC)
R-Value Work: 0.244 (Depositor), 0.251 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.087	α = 90
b = 108.087	β = 90
c = 225.199	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31722040
National Natural Science Foundation of China (NSFC)	China	31771935
National Natural Science Foundation of China (NSFC)	China	31901628

Revision History (Full details and data files)

Version 1.0: 2022-10-12
Type: Initial release
Version 1.1: 2024-04-03
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.