4XV0 | pdb_00004xv0

Crystal structure of an endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Trichoderma reesei

• PDB DOI: https://doi.org/10.2210/pdb4XV0/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma reesei QM6a
• Expression System: Aspergillus niger
• Mutation(s): No 


• Deposited: 2015-01-26 Released: 2015-02-11 
• Deposition Author(s): Stogios, P.J., Xu, X., Cui, H., Savchenko, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.122 (Depositor), 0.124 (DCC) 
• R-Value Observed: 
  0.125 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Trichoderma reesei

Stogios, P.J., Xu, X., Cui, H., Savchenko, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.96 kDa 
• Atom Count: 2,867 
• Modeled Residue Count: 302 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A	302	Trichoderma reesei QM6a	Mutation(s): 0  Gene Names: TRIREDRAFT_120229 EC: 3.2.1.8
UniProt
Find proteins for G0RA32 (Hypocrea jecorina (strain QM6a)) Explore G0RA32  Go to UniProtKB:  G0RA32

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.122 (Depositor), 0.124 (DCC) 
• R-Value Observed: 0.125 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.708	α = 90
b = 47.49	β = 90
c = 136.403	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Stogios, P.J., Xu, X., Cui, H., Savchenko, A.

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 2.0: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy
• Version 2.1: 2024-11-20
  Changes: Structure summary