5DLC | pdb_00005dlc

X-ray Crystal Structure of a Pyridoxine 5-prime-phosphate synthase from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb5DLC/pdb

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

Deposited: 2015-09-04 Released: 2015-09-16
Deposition Author(s): Fairman, J.W., Abendroth, J., Lorimer, D., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.212 (Depositor), 0.210 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5DLC

This is version 1.3 of the entry. See complete history.

Literature

X-ray Crystal Structure of a Pyridoxine 5-prime-phosphate synthase from Pseudomonas aeruginosa

Fairman, J.W., Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 113.42 kDa
Atom Count: 7,593
Modeled Residue Count: 968
Deposited Residue Count: 1,024
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxine 5'-phosphate synthase	A, B, C, D	256	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: pdxJ EC: 2.6.99.2
UniProt
Find proteins for Q02HS5 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore Q02HS5 Go to UniProtKB: Q02HS5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02HS5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.212 (Depositor), 0.210 (DCC)
R-Value Work: 0.173 (Depositor), 0.173 (DCC)
R-Value Observed: 0.175 (Depositor)

Diffraction Data:

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.46	α = 90
b = 150.46	β = 90
c = 86.57	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
BALBES	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-09-16

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2015-09-16
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.