1GW1

Substrate distortion by beta-mannanase from Pseudomonas cellulosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Substrate Distortion by a Beta-Mannanase: Snapshots of the Michaelis and Covalent-Intermediate Complexes Suggest a B2,5 Conformation for the Transition State

Ducros, V.Zechel, D.L.Murshudov, G.Gilbert, H.J.Szabo, L.Stoll, D.Withers, S.G.Davies, G.J.

(2002) Angew Chem Int Ed Engl 41: 2824


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MANNAN ENDO-1,4-BETA-MANNOSIDASEA376Cellvibrio japonicusMutation(s): 1 
EC: 3.2.1.78
UniProt
Find proteins for P49424 (Cellvibrio japonicus (strain Ueda107))
Explore P49424 
Go to UniProtKB:  P49424
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-mannopyranoseB4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G78273IU
GlyCosmos:  G78273IU
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NIN (Subject of Investigation/LOI)
Query on NIN

Download Ideal Coordinates CCD File 
F [auth A]DINITROPHENYLENE
C6 H4 N2 O4
WDCYWAQPCXBPJA-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
G [auth A], H [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.488α = 90
b = 93.488β = 90
c = 53.719γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-05
    Type: Initial release
  • Version 1.1: 2012-11-28
    Changes: Database references, Other, Source and taxonomy, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary