2DCK | pdb_00002dck

A tetragonal-lattice structure of alkaliphilic XynJ from Bacillus sp. 41M-1

• PDB DOI: https://doi.org/10.2210/pdb2DCK/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. 41M-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-01-07 Released: 2007-03-20 
• Deposition Author(s): Fibriansah, G., Ihsanawati, Tanaka, N., Nakamura, S., Kumasaka, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.198 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

A two-domain structure of alkaliphilic XynJ from Bacillus sp. 41M-1

Ihsanawati, Tanaka, N., Nakamura, S., Kumasaka, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.48 kDa 
• Atom Count: 2,857 
• Modeled Residue Count: 320 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
xylanase J	A	354	Bacillus sp. 41M-1	Mutation(s): 0  Gene Names: xynJ EC: 3.2.1.8
UniProt
Find proteins for Q9RC94 (Bacillus sp. 41M-1) Explore Q9RC94  Go to UniProtKB:  Q9RC94

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.198 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.579	α = 90
b = 116.579	β = 90
c = 45.909	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Fibriansah, G., Ihsanawati, Tanaka, N., Nakamura, S., Kumasaka, T.

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description