3JUG

Crystal structure of endo-beta-1,4-mannanase from the alkaliphilic Bacillus sp. N16-5

• PDB DOI: https://doi.org/10.2210/pdb3JUG/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. N16-5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-15 Released: 2010-09-15 
• Deposition Author(s): Zhao, Y., Zhang, Y., Xue, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.215 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Structure Analysis of Alkaline beta-mannanase from Alkaliphilic Bacillus sp. N16-5 Implications for Adaptation to Alkaline Conditions

Zhao, Y., Zhang, Y., Cao, Y., Qi, J., Xue, Y., Gao, F., Peng, H., Gao, G.F., Ma, Y.

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: 38.26 kDa 
• Atom Count: 2,905 
• Modelled Residue Count: 294 
• Deposited Residue Count: 345 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-mannanase	A	345	Bacillus sp. N16-5	Mutation(s): 0  Gene Names: manA EC: 3.2.1.78
UniProt
Find proteins for Q5YEX6 (Bacillus sp. N16-5) Explore Q5YEX6  Go to UniProtKB:  Q5YEX6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.215 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.033	α = 90
b = 63.312	β = 90
c = 83.342	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Zhao, Y., Zhang, Y., Xue, Y.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description