3VPL | pdb_00003vpl

Crystal structure of a 2-fluoroxylotriosyl complex of the Vibrio sp. AX-4 Beta-1,3-xylanase

• PDB DOI: https://doi.org/10.2210/pdb3VPL/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-05 Released: 2013-03-06 
• Deposition Author(s): Watanabe, N., Sakaguchi, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.156 (Depositor), 0.155 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of a 2-fluoroxylotriosyl complex of the Vibrio sp. AX-4 beta-1,3-xylanase at 1.2 A resolution

Sakaguchi, K., Goddard-Borger, E.D., Kawamura, T., Kiyohara, M., Tanaka, I., Ito, M., Withers, S.G., Watanabe, N.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 37.95 kDa 
• Atom Count: 3,278 
• Modeled Residue Count: 324 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-1,3-xylanase XYL4	A	333	Vibrio sp.	Mutation(s): 0  Gene Names: xyl4 EC: 3.2.1.32
UniProt
Find proteins for D5MP61 (Vibrio sp) Explore D5MP61  Go to UniProtKB:  D5MP61
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-3)-beta-D-xylopyranose-(1-3)-2-deoxy-2-fluoro-beta-D-xylopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G18138CS GlyCosmos: G18138CS

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-3)-2-deoxy-2-fluoro-beta-D-xylopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan: G94440QL GlyCosmos: G94440QL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DNX	D [auth A]	3,4-dinitrophenol C6 H4 N2 O5 AKLOLDQYWQAREW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.156 (Depositor), 0.155 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.343	α = 90
b = 75.437	β = 90
c = 81.646	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
KEK-PF	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Watanabe, N., Sakaguchi, K.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• 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: 2023-11-08
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary