2G3J | pdb_00002g3j

Structure of S.olivaceoviridis xylanase Q88A/R275A mutant

• PDB DOI: https://doi.org/10.2210/pdb2G3J/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces olivaceoviridis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-02-20 Released: 2007-03-06 
• Deposition Author(s): Diertavitian, S., Kaneko, S., Fujimoto, Z., Kuno, A., Johansson, E., Lo Leggio, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.223 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.175 (DCC) 

Literature

Structure-based engineering of glucose specificity in a family 10 xylanase from Streptomyces olivaceoviridis E-86

Ichinose, H., Diertavitian, S., Fujimoto, Z., Kuno, A., Leggio, L.L., Kaneko, S.

(2012) Process Biochem 47: 358-365

• DOI: https://doi.org/10.1016/j.procbio.2011.06.002

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.17 kDa 
• Atom Count: 2,451 
• Modeled Residue Count: 301 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylanase	A	313	Streptomyces olivaceoviridis	Mutation(s): 2  EC: 3.2.1.8
UniProt
Find proteins for Q7SI98 (Streptomyces olivaceoviridis) Explore Q7SI98  Go to UniProtKB:  Q7SI98

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose	B, C	2		N/A
Glycosylation Resources
GlyTouCan: G92719DV GlyCosmos: G92719DV

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.223 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.175 (DCC) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.953	α = 90
b = 119.953	β = 90
c = 55.216	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-06 
Deposition Author(s): Diertavitian, S., Kaneko, S., Fujimoto, Z., Kuno, A., Johansson, E., Lo Leggio, L.

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-02-29
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary