6MDY

Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Legionella pneumophila Philadelphia 1

PDB DOI: https://doi.org/10.2210/pdb6MDY/pdb

Classification: HYDROLASE
Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-09-05 Released: 2018-09-19
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.227
R-Value Work: 0.176
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Currently 6MDY does not have a validation slider image.

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

Literature

Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Legionella pneumophila Philadelphia 1

Edwards, T.E., Dranow, D.M., Lorimer, D.D., Horanyi, P.S., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 124.19 kDa
Atom Count: 7,439
Modelled Residue Count: 978
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxyphosphooctonate aldolase	A, B, C, D	282	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0 Gene Names: kdsA, lpg1182 EC: 2.5.1.55
UniProt
Find proteins for Q5ZWA3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZWA3 Go to UniProtKB: Q5ZWA3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZWA3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.227
R-Value Work: 0.176
R-Value Observed: 0.179
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/m36mdy

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.52	α = 90
b = 87.32	β = 90
c = 160.52	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

View Full Validation Report

Currently 6MDY does not have a validation slider image.

Entry History

Deposition Data

Released Date: 2018-09-19

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-09-19
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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.