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), 0.132 (DCC)
R-Value Work:
0.125 (Depositor), 0.127 (DCC)
R-Value Observed:
0.125 (Depositor)

Starting Model: experimental
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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.132 (DCC)
R-Value Work: 0.125 (Depositor), 0.127 (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

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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

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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.