Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 95.99 kDa 
• Atom Count: 7366 
• Modelled Residue Count: 872 
• Deposited Residue Count: 872 
• Unique protein chains: 1

1V6U

Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E-86 Complexed With 2(2)-alpha-L-arabinofuranosyl-xylobiose

• PDB DOI: 10.2210/pdb1V6U/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces olivaceoviridis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-04 Released: 2004-04-27 
• Deposition Author(s): Fujimoto, Z., Kaneko, S., Kuno, A., Kobayashi, H., Kusakabe, I., Mizuno, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.253 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Literature

Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86

Fujimoto, Z., Kaneko, S., Kuno, A., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2004) J Biol Chem 279: 9606-9614

• PubMed: 14670957 
• DOI: 10.1074/jbc.M312293200
• Primary Citation of Related Structures:  
  1V6U, 1V6V, 1V6W, 1V6X


• PubMed Abstract: 
  

The family 10 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn10A) consists of a GH10 catalytic domain, which is joined by a Gly/Pro-rich linker to a family 13 carbohydrate-binding module (CBM13) that interacts with xylan. To understand how GH10 xylanases and CBM13 recognize decorated xylans, the crystal structure of SoXyn10A was determined in complex with alpha-l-arabinofuranosyl- and 4-O-methyl-alpha-d-glucuronosyl-xylooligosaccharides. The bound sugars were observed in the subsites of the catalytic cleft and also in subdomains alpha and gamma of CBM13. The data reveal that the binding mode of the oligosaccharides in the active site of the catalytic domain is entirely consistent with the substrate specificity and, in conjunction with the accompanying paper, demonstrate that the accommodation of the side chains in decorated xylans is conserved in GH10 xylanases of SoXyn10A against arabinoglucuronoxylan. CBM13 was shown to bind xylose or xylooligosaccharides reversibly by using nonsymmetric sugars as the ligands. The independent multiple sites in CBM13 may increase the probability of substrate binding.

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Organizational Affiliation: 

Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
endo-1,4-beta-D-xylanase	A, B	436	Streptomyces olivaceoviridis	Mutation(s): 0  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	Chain Length	2D Diagram	Glycosylation
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C, D, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G87728WL GlyCosmos:  G87728WL

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-arabinofuranose-(1-3)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	E, F	3		N/A
Glycosylation Resources
GlyTouCan:  G96828DL GlyCosmos:  G96828DL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYS	J [auth A]	alpha-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-LECHCGJUSA-N
XYP	I [auth A], K [auth B]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116	C, D, G, H	4beta-beta-xylobiose	Oligosaccharide / Metabolism		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.253 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.29	α = 90
b = 94.23	β = 90
c = 137.69	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-04 
• Released Date: 2004-04-27 
Deposition Author(s): Fujimoto, Z., Kaneko, S., Kuno, A., Kobayashi, H., Kusakabe, I., Mizuno, H.

Revision History  

• Version 1.0: 2004-04-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary