8QK4 | pdb_00008qk4

Dehydratase domain (PksJ DH1) from the bacillaene trans-AT PKS

PDB DOI: https://doi.org/10.2210/pdb8QK4/pdb

Classification: LYASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-09-14 Released: 2024-09-25
Deposition Author(s): Pang, F., Alkhalaf, L.M., Jenner, M.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), UK Research and Innovation (UKRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.216 (Depositor), 0.224 (DCC)
R-Value Work:
0.176 (Depositor), 0.186 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8QK4

This is version 1.0 of the entry. See complete history.

Literature

Dehydratase domain (PksJ DH1) from the bacillaene trans-AT PKS

Pang, F., Alkhalaf, L.M., Jenner, M.

To be published.

Macromolecule Content

Total Structure Weight: 74.73 kDa
Atom Count: 4,607
Modeled Residue Count: 567
Deposited Residue Count: 682
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase PksJ	A, B	341	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: pksJ, pksK, BSU17180
UniProt
Find proteins for P40806 (Bacillus subtilis (strain 168)) Explore P40806 Go to UniProtKB: P40806
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40806
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.216 (Depositor), 0.224 (DCC)
R-Value Work: 0.176 (Depositor), 0.186 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.905	α = 90
b = 84.79	β = 90
c = 131.938	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R012121/1
UK Research and Innovation (UKRI)	United Kingdom	MR/W011247/1

Revision History (Full details and data files)

Version 1.0: 2024-09-25
Type: Initial release

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