6KVV | pdb_00006kvv

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

• PDB DOI: https://doi.org/10.2210/pdb6KVV/pdb

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


• Deposited: 2019-09-05 Released: 2021-07-14 
• Deposition Author(s): Li, C., Wan, Q.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 
  0.159 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism

Wan, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.92 kDa 
• Atom Count: 1,924 
• Modeled Residue Count: 190 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase 2	A	190	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

Oligosaccharides

Help

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL (Subject of Investigation/LOI)	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900117	B	4beta-beta-xylotriose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free:  0.159 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.679	α = 90
b = 67.931	β = 90
c = 78.81	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Li, C., Wan, Q.

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

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description