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), 0.208 (DCC)
R-Value Work:
0.176 (Depositor), 0.185 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.208 (DCC)
R-Value Work: 0.176 (Depositor), 0.185 (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

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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

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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.