5ZMP

The structure of a lysine deacylase

PDB DOI: https://doi.org/10.2210/pdb5ZMP/pdb

Classification: HYDROLASE
Organism(s): Picosynechococcus sp. PCC 73109
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-05 Released: 2019-02-06
Deposition Author(s): Ge, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.215
R-Value Work: 0.173

wwPDB Validation 3D Report Full Report

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

Literature

The structure of a lysine deacylase

Ge, F.

To be published.

Macromolecule Content

Total Structure Weight: 34.16 kDa
Atom Count: 2,614
Modelled Residue Count: 305
Deposited Residue Count: 307
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lysine deacylase	A	307	Picosynechococcus sp. PCC 73109	Mutation(s): 0 Gene Names: SYNPCC7002_A2791
UniProt
Find proteins for B1XMP1 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6)) Explore B1XMP1 Go to UniProtKB: B1XMP1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1XMP1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 2.19 Å
R-Value Free: 0.215
R-Value Work: 0.173
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.79	α = 90
b = 56.79	β = 90
c = 112.52	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-02-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-02-06
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 R01GM133198.