4XUY | pdb_00004xuy

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

• PDB DOI: https://doi.org/10.2210/pdb4XUY/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus niger CBS 513.88
• Expression System: Aspergillus niger CBS 513.88
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

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

Stogios, P.J., Dong, A., 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.21 kDa 
• Atom Count: 5,346 
• Modeled Residue Count: 604 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable endo-1,4-beta-xylanase C	A, B	302	Aspergillus niger CBS 513.88	Mutation(s): 0  Gene Names: xlnC, xynA, An03g00940 EC: 3.2.1.8
UniProt
Find proteins for A2QFV7 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513)) Explore A2QFV7  Go to UniProtKB:  A2QFV7

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.585	α = 83.19
b = 50.685	β = 87.31
c = 59.097	γ = 61.66

Software Package:

Software Name	Purpose
HKL-3000	data reduction
PHASER	phasing
HKL-3000	data scaling
Coot	model building
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Advisory, Derived calculations, Refinement description, Source and taxonomy
• Version 2.0: 2023-09-27
  Changes: Data collection, Database references, Polymer sequence, Refinement description
• Version 2.1: 2024-11-13
  Changes: Structure summary