7EO3

X-ray structure analysis of beita-1,3-glucanase

PDB DOI: https://doi.org/10.2210/pdb7EO3/pdb

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

Deposited: 2021-04-21 Released: 2022-03-02
Deposition Author(s): Wan, Q., Feng, J., Xu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free:
0.162 (Depositor), 0.160 (DCC)
R-Value Work:
0.143 (Depositor), 0.140 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Identification and structural analysis of a thermophilic beta-1,3-glucanase from compost

Feng, J., Xu, S., Feng, R., Kovalevsky, A., Zhang, X., Liu, D., Wan, Q.

(2021) Bioresour Bioprocess 8: 102-102

DOI: https://doi.org/10.1186/s40643-021-00449-4

Macromolecule Content

Total Structure Weight: 31.01 kDa
Atom Count: 2,527
Modelled Residue Count: 282
Deposited Residue Count: 283
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,3-beta-glucanase	A	283	Actinomycetes bacterium	Mutation(s): 0 Gene Names: DIU60_04100
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free: 0.162 (Depositor), 0.160 (DCC)
R-Value Work: 0.143 (Depositor), 0.140 (DCC)
R-Value Observed: 0.144 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.397	α = 90
b = 61.01	β = 90
c = 70.672	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2022-03-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-03-02
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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.