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.

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), 0.184 (DCC)

Starting Model: experimental
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This is version 1.6 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 45.56 kDa
Atom Count: 3,310
Modeled Residue Count: 399
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39116
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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), 0.184 (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

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Entry History

Deposition Data

Released Date: 1998-08-12

Deposition Author(s):

Pickersgill, R.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.