8QZY | pdb_00008qzy

Structural and biochemical characterization of diaminopimelate epimerase from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb8QZY/pdb

Classification: ISOMERASE
Organism(s): Pseudomonas aeruginosa PA14
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-30 Released: 2024-11-06
Deposition Author(s): Schneider, P., Blankenfeldt, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.217 (Depositor), 0.229 (DCC)
R-Value Work:
0.177 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Structural and biochemical characterization of diaminopimelate epimerase from Pseudomonas aeruginosa

Schneider, P., Blankenfeldt, W.

To be published.

Macromolecule Content

Total Structure Weight: 61.01 kDa
Atom Count: 4,636
Modeled Residue Count: 554
Deposited Residue Count: 556
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate epimerase	A, B	278	Pseudomonas aeruginosa PA14	Mutation(s): 0 Gene Names: dapF, PA14_69690 EC: 5.1.1.7
UniProt
Find proteins for Q51564 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q51564 Go to UniProtKB: Q51564
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q51564
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.217 (Depositor), 0.229 (DCC)
R-Value Work: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.542	α = 90
b = 88.58	β = 90
c = 97.128	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-06

Deposition Author(s):

Blankenfeldt, W.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-11-06
Type: Initial release

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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.