1V0K

Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-deoxynojirimycin at pH 5.8

• PDB DOI: https://doi.org/10.2210/pdb1V0K/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces lividans
• Expression System: Streptomyces lividans
• Mutation(s): No 


• Deposited: 2004-03-31 Released: 2004-08-16 
• Deposition Author(s): Gloster, T.M., Williams, S.J., Roberts, S., Tarling, C.A., Wicki S, J., Withers, G., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 0.137 
• R-Value Work: 0.114 
• R-Value Observed: 0.115 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 34.41 kDa 
• Atom Count: 3,238 
• Modelled Residue Count: 302 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-BETA-XYLANASE A	A	313	Streptomyces lividans	Mutation(s): 0  EC: 3.2.1.8
UniProt
Find proteins for P26514 (Streptomyces lividans) Explore P26514  Go to UniProtKB:  P26514

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYP	B [auth A]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N
XDN	C [auth A]	PIPERIDINE-3,4,5-TRIOL C5 H11 N O3 RMCNETIHECSPMZ-SCDXWVJYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 0.137 
• R-Value Work: 0.114 
• R-Value Observed: 0.115 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.08	α = 90
b = 46.204	β = 90
c = 86.071	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-16 
Deposition Author(s): Gloster, T.M., Williams, S.J., Roberts, S., Tarling, C.A., Wicki S, J., Withers, G., Davies, G.J.

Revision History  

• Version 1.0: 2004-08-16
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary