5X2I | pdb_00005x2i

Polygalacturonate Lyase by Fusing with a Self-assembling Amphipathic Peptide

PDB DOI: https://doi.org/10.2210/pdb5X2I/pdb

Classification: LYASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-01-31 Released: 2018-08-08
Deposition Author(s): Zhao, W.X.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.200 (Depositor), 0.210 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Polygalacturonate Lyase by Fusing with a Self-assembling Amphipathic Peptide

Zhao, W.X.

To be published.

Macromolecule Content

Total Structure Weight: 43.52 kDa
Atom Count: 3,237
Modeled 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 subsp. subtilis str. 168	Mutation(s): 0 Gene Names: pel, BSU07560 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 2 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]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.200 (Depositor), 0.210 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.094	α = 67.51
b = 51.212	β = 74.93
c = 51.296	γ = 78.75

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-08-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31401638

Revision History (Full details and data files)

Version 1.0: 2018-08-08
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.