2O0W

Pectate lyase bound to hexasaccharide compound IV

PDB DOI: https://doi.org/10.2210/pdb2O0W/pdb

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

Deposited: 2006-11-28 Released: 2007-11-20
Deposition Author(s): Pickersgill, R.W., Seyedarabi, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.198
R-Value Work: 0.154
R-Value Observed: 0.156

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural and thermodynamic insights into the mechanism of pectate lyase

Seyedarabi, A., Hussain, S., Fries, M., MacDoughall, A., Cummings, N., Smith, D., Worboys, K., Brocklehurst, K., Pickersgill, R.W.

To be published.

Macromolecule Content

Total Structure Weight: 43.48 kDa
Atom Count: 3,701
Modelled Residue Count: 399
Deposited Residue Count: 399
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectate lyase	A	399	Bacillus subtilis	Mutation(s): 1 Gene Names: pel 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.198
R-Value Work: 0.154
R-Value Observed: 0.156
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.725	α = 90
b = 68.956	β = 112.7
c = 59.482	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Pickersgill, R.W.

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2015-06-24
Changes: Data collection
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-12-27
Changes: Data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.