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Crystal structure of alkaline mannanase from Bacillus sp. strain JAMB-602: catalytic domain and its Carbohydrate Binding Module


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallization and preliminary X-ray study of alkaline mannanase from an alkaliphilic Bacillus isolate.

Akita, M.Takeda, N.Hirasawa, K.Sakai, H.Kawamoto, M.Yamamoto, M.Grant, W.D.Hatada, Y.Ito, S.Horikoshi, K.

(2004) Acta Crystallogr.,Sect.D 60: 1490-1492

  • DOI: 10.1107/S0907444904014313

  • PubMed Abstract: 
  • An alkaline mannanase (EC 3.2.1.78) from the alkaliphilic Bacillus sp. strain JAMB-602 was cloned and sequenced. The deduced amino-acid sequence of the enzyme suggested that the enzyme consists of a catalytic and unknown additional domains. The recom ...

    An alkaline mannanase (EC 3.2.1.78) from the alkaliphilic Bacillus sp. strain JAMB-602 was cloned and sequenced. The deduced amino-acid sequence of the enzyme suggested that the enzyme consists of a catalytic and unknown additional domains. The recombinant enzyme expressed by B. subtilis was crystallized using the hanging-drop vapour-diffusion method at 277 K. X-ray diffraction data were collected to 1.65 A. The crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 70.7, b = 79.5, c = 80.4 A. The asymmetric unit contains one protein molecule, with a corresponding VM of 2.26 A3 Da(-1) and a solvent content of 45.6%. Molecular replacement for initial phasing was carried out using the three-dimensional structure of a mannanase from Thermomonospora fusca as a search model, which corresponds to the catalytic domain of the alkaline mannanase. It gave sufficient phases to build the unknown domain.


    Organizational Affiliation

    Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka 237-0061. akitam@jamstec.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
endo-beta-1,4-Mannanase
A
464Bacillus sp. JAMB-602Mutation(s): 0 
Gene Names: amn5A
Find proteins for Q4W8M3 (Bacillus sp. JAMB-602)
Go to UniProtKB:  Q4W8M3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.682α = 90.00
b = 79.480β = 90.00
c = 80.418γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance