5OYD

GH5 endo-xyloglucanase from Cellvibrio japonicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

In vitro and in vivo characterization of threeCellvibrio japonicusglycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions.

Attia, M.A.Nelson, C.E.Offen, W.A.Jain, N.Davies, G.J.Gardner, J.G.Brumer, H.

(2018) Biotechnol Biofuels 11: 45-45


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellulase, putative, cel5D
A, B
396Cellvibrio japonicus (strain Ueda107)Mutation(s): 0 
Gene Names: cel5D
EC: 3.2.1.4
Find proteins for B3PD52 (Cellvibrio japonicus (strain Ueda107))
Go to UniProtKB:  B3PD52
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
A, B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
XYS
Query on XYS

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Download CCD File 
A, B
XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
 Ligand Interaction
NBG
Query on NBG

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Download CCD File 
A, B
1-N-ACETYL-BETA-D-GLUCOSAMINE
C8 H15 N O6
IBONACLSSOLHFU-JAJWTYFOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.455α = 90.00
b = 97.598β = 90.00
c = 157.196γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
DIALSdata reduction
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-28
    Type: Database references
  • Version 1.2: 2018-03-28
    Type: Data collection, Database references