1VBL | pdb_00001vbl

Structure of the thermostable pectate lyase PL 47

• PDB DOI: https://doi.org/10.2210/pdb1VBL/pdb

• Classification: LYASE
• Organism(s): Bacillus sp. TS-47
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2004-02-27 Released: 2005-04-19 
• Deposition Author(s): Nakaniwa, T., Tada, T., Yamaguchi, A., Kitatani, T., Takao, M., Sakai, T., Nishimura, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Structural Basis for Thermostability of Pectate Lyase from Bacillus sp. TS 47

Nakaniwa, T., Tada, T., Yamaguchi, A., Kitatani, T., Takao, M., Sakai, T., Nishimura, K.

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: 47.36 kDa 
• Atom Count: 3,712 
• Modeled Residue Count: 416 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pectate lyase 47	A	416	Bacillus sp. TS-47	Mutation(s): 0  EC: 4.2.2.2
UniProt
Find proteins for Q9AJM4 (Bacillus sp. TS-47) Explore Q9AJM4  Go to UniProtKB:  Q9AJM4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.61	α = 90
b = 58.61	β = 90
c = 229.42	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-19 
Deposition Author(s): Nakaniwa, T., Tada, T., Yamaguchi, A., Kitatani, T., Takao, M., Sakai, T., Nishimura, K.

Revision History  

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-04-23
  Changes: Experimental preparation
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations