5G1F

Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from Bacillus subtilis in complex with coenzyme A

PDB DOI: https://doi.org/10.2210/pdb5G1F/pdb

Classification: LIGASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-03-25 Released: 2017-03-08
Deposition Author(s): Moynie, L., Wang, M., Campopiano, D.J., Naismith, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 ?
R-Value Free: 0.252
R-Value Work: 0.217
R-Value Observed: 0.219

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

The Structure of the 6-Carboxyhexanoate-Coa Ligase from Bacillus Subtilis

Wang, M., Moynie, L., Campopiano, D.J., Naismith, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 60.85 kDa
Atom Count: 4,060
Modelled Residue Count: 493
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-CARBOXYHEXANOATE-COA LIGASE	A, B	260	Bacillus subtilis	Mutation(s): 0 EC: 6.2.1.14
UniProt
Find proteins for P53559 (Bacillus subtilis (strain 168)) Explore P53559 Go to UniProtKB: P53559
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53559
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
2PE Query on 2PE Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PML Query on PML Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	PIMELIC ACID C₇ H₁₂ O₄ WLJVNTCWHIRURA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 ?
R-Value Free: 0.252
R-Value Work: 0.217
R-Value Observed: 0.219
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 50.59	α = 90
b = 78.36	β = 90
c = 166.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data reduction
xia2	data scaling
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-03-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-03-08
Type: Initial release
Version 2.0: 2017-06-21
Changes: Advisory, Atomic model, Derived calculations
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Other, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

5G1F

Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from Bacillus subtilis in complex with coenzyme A

The Structure of the 6-Carboxyhexanoate-Coa Ligase from Bacillus Subtilis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)