6S62 | pdb_00006s62

Crystal structure of 2-methylcitrate dehydratase (PrpD) from Pseudomonas aeruginosa in apo form.

PDB DOI: https://doi.org/10.2210/pdb6S62/pdb

Classification: ISOMERASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-02 Released: 2020-10-14
Deposition Author(s): Wijaya, A.J., Brear, P., Dolan, S.K., Welch, M.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.260 (Depositor), 0.260 (DCC)
R-Value Work:
0.206 (Depositor), 0.208 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of 2-methylcitrate dehydratase (PrpD) from Pseudomonas aeruginosa in apo form.

Wijaya, A.J., Brear, P., Dolan, S.K., Welch, M.

To be published.

Macromolecule Content

Total Structure Weight: 329.72 kDa
Atom Count: 22,926
Modeled Residue Count: 2,906
Deposited Residue Count: 2,964
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionate catabolic protein PrpD	A, B, C, D, E A, B, C, D, E, F	494	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: prpD, PA0792 EC: 4.2.1.79
UniProt
Find proteins for Q9I5E6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I5E6 Go to UniProtKB: Q9I5E6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I5E6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.260 (Depositor), 0.260 (DCC)
R-Value Work: 0.206 (Depositor), 0.208 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.48	α = 90
b = 124.54	β = 116.85
c = 126.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M019411/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/R005435/1

Revision History (Full details and data files)

Version 1.0: 2020-10-14
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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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.