5ZH0 | pdb_00005zh0

Crystal Structures of Endo-beta-1,4-xylanase II

PDB DOI: https://doi.org/10.2210/pdb5ZH0/pdb

Classification: HYDROLASE
Organism(s): Trichoderma reesei RUT C-30
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-03-10 Released: 2019-03-13
Deposition Author(s): Zhang, X., Wan, Q., Li, Z.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free:
0.130 (Depositor), 0.130 (DCC)
R-Value Work:
0.125 (Depositor), 0.120 (DCC)
R-Value Observed:
0.125 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structures of Endo-beta-1,4-xylanase II

Zhang, X., Wan, Q., Li, Z.

To be published.

Macromolecule Content

Total Structure Weight: 20.95 kDa
Atom Count: 1,818
Modeled Residue Count: 189
Deposited Residue Count: 189
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase 2	A	189	Trichoderma reesei RUT C-30	Mutation(s): 0 Gene Names: xyn2, M419DRAFT_124931 EC: 3.2.1.8
UniProt
Find proteins for P36217 (Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30)) Explore P36217 Go to UniProtKB: P36217
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36217
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD 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]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free: 0.130 (Depositor), 0.130 (DCC)
R-Value Work: 0.125 (Depositor), 0.120 (DCC)
R-Value Observed: 0.125 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.403	α = 90
b = 59.082	β = 90
c = 69.926	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-03-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31670790

Revision History (Full details and data files)

Version 1.0: 2019-03-13
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.