8X66 | pdb_00008x66

Crystal structure of triple mutant X11P(P71T+N13F+Q34L) xylanase from a metagenome derived gene from sugarcane bagasse collection site

PDB DOI: https://doi.org/10.2210/pdb8X66/pdb

Classification: HYDROLASE
Organism(s): uncultured bacterium
Expression System: Escherichia
Mutation(s): Yes

Deposited: 2023-11-20 Released: 2024-11-27
Deposition Author(s): Chitnumsub, P., Jaruwat, A., Boonyapakron, K., Prabmark, K.
Funding Organization(s): National Center for Genetic Engineering and Biotechnology (Thailand)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.243 (Depositor), 0.244 (DCC)
R-Value Work:
0.192 (Depositor), 0.197 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Engineered hyperthermophilic xylanase from bagasse metagenome and its basis of thermophilicity by molecular dynamic simulation

Boonyapakron, K.

To be published.

Macromolecule Content

Total Structure Weight: 68.88 kDa
Atom Count: 4,837
Modeled Residue Count: 577
Deposited Residue Count: 621
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A, B, C	207	uncultured bacterium	Mutation(s): 3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.243 (Depositor), 0.244 (DCC)
R-Value Work: 0.192 (Depositor), 0.197 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.689	α = 90
b = 105.689	β = 90
c = 70.165	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Boonyapakron, K.

Funding Organization	Location	Grant Number
National Center for Genetic Engineering and Biotechnology (Thailand)	Thailand	B16F640052

Revision History (Full details and data files)

Version 1.0: 2024-11-27
Type: Initial release

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.