5ZF3 | pdb_00005zf3

Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xylotriose

PDB DOI: https://doi.org/10.2210/pdb5ZF3/pdb

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

Deposited: 2018-03-02 Released: 2019-03-06
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: 1.20 Å
R-Value Free:
0.144 (Depositor), 0.134 (DCC)
R-Value Work:
0.133 (Depositor), 0.131 (DCC)
R-Value Observed:
0.133 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xylotriose

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

To be published.

Macromolecule Content

Total Structure Weight: 21.49 kDa
Atom Count: 1,865
Modeled Residue Count: 189
Deposited Residue Count: 189
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36217
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G87429QT GlyCosmos: G87429QT

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 E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900117 Query on PRD_900117	B	4beta-beta-xylotriose	Oligosaccharide / Metabolism		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.144 (Depositor), 0.134 (DCC)
R-Value Work: 0.133 (Depositor), 0.131 (DCC)
R-Value Observed: 0.133 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.413	α = 90
b = 58.492	β = 90
c = 69.281	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-06

Deposition Author(s):

Zhang, X.

Wan, Q.

Li, Z.

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

Revision History (Full details and data files)

Version 1.0: 2019-03-06
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary