7XW1 | pdb_00007xw1

The crystal structure of AhpD from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb7XW1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-25 Released: 2022-06-29
Deposition Author(s): Xu, B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.313 (Depositor), 0.310 (DCC)
R-Value Work:
0.249 (Depositor), 0.250 (DCC)
R-Value Observed:
0.255 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of AhpD from Pseudomonas aeruginosa

Xu, B.

To be published.

Macromolecule Content

Total Structure Weight: 16.25 kDa
Atom Count: 999
Modeled Residue Count: 133
Deposited Residue Count: 145
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxymuconolactone decarboxylase family protein	A	145	Pseudomonas aeruginosa	Mutation(s): 0 EC: 1.11.1.15
UniProt
Find proteins for A0A2U2XNT2 (Pseudomonas aeruginosa) Explore A0A2U2XNT2 Go to UniProtKB: A0A2U2XNT2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2U2XNT2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.313 (Depositor), 0.310 (DCC)
R-Value Work: 0.249 (Depositor), 0.250 (DCC)
R-Value Observed: 0.255 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.976	α = 90
b = 92.976	β = 90
c = 65.957	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-06-29
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary

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.