2BSP | pdb_00002bsp

BACILLUS SUBTILIS PECTATE LYASE R279K MUTANT

• PDB DOI: https://doi.org/10.2210/pdb2BSP/pdb

• Classification: LYASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 1998-07-31 Released: 1998-08-12 
• Deposition Author(s): Pickersgill, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.225 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

The Conserved Arginine Proximal to the Essential Calcium of Bacillus Subtilis Pectate Lyase Stabilizes the Transition State

Pickersgill, R., Worboys, K., Scott, M., Cummings, N., Cooper, A., Jenkins, J., Smith, D.

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: 45.56 kDa 
• Atom Count: 3,310 
• Modelled Residue Count: 399 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PECTATE LYASE)	A	420	Bacillus subtilis	Mutation(s): 1  EC: 4.2.2.2
UniProt
Find proteins for P39116 (Bacillus subtilis (strain 168)) Explore P39116  Go to UniProtKB:  P39116

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: 1.80 Å
• R-Value Free:  0.225 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.180 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.43	α = 90
b = 69.71	β = 112.65
c = 60.23	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
ROTAVATA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-08-12 
Deposition Author(s): Pickersgill, R.

Revision History  

• Version 1.0: 1998-08-12
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-14
  Changes: Data collection
• Version 1.6: 2024-04-03
  Changes: Refinement description