4U4B | pdb_00004u4b

Crystal Structure of Pectate Lyase Pel3 from Pectobacterium carotovorum with one monomer in the A.U.

PDB DOI: https://doi.org/10.2210/pdb4U4B/pdb

Classification: LYASE
Organism(s): Pectobacterium carotovorum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-07-23 Released: 2015-08-05
Deposition Author(s): Ballut, L., Gouet, P., Shevchik, V.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.250 (Depositor), 0.251 (DCC)
R-Value Work:
0.170 (Depositor), 0.175 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Pectate Lyase Pel3 from Pectobacterium carotovorum with one monomer in the A.U.

Ballut, L., Gouet, P., Schevchik, V.E., Pineau, C., Guschinskaya, N.

To be published.

Macromolecule Content

Total Structure Weight: 37.37 kDa
Atom Count: 2,630
Modeled Residue Count: 326
Deposited Residue Count: 347
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectate lyase	A	347	Pectobacterium carotovorum	Mutation(s): 0 Gene Names: pel-3 EC: 4.2.2.2
UniProt
Find proteins for Q47465 (Pectobacterium carotovorum) Explore Q47465 Go to UniProtKB: Q47465
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q47465
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.250 (Depositor), 0.251 (DCC)
R-Value Work: 0.170 (Depositor), 0.175 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37	α = 90
b = 44.35	β = 93.58
c = 86.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-08-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-08-05
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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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.