7P2X | pdb_00007p2x

E.coli GyrB24 with inhibitor KOB20 (EBL2583)

PDB DOI: https://doi.org/10.2210/pdb7P2X/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-06 Released: 2022-07-20
Deposition Author(s): Stevenson, C.E.M., Lawson, D.M., Maxwell, A.M., Henderson, S.R., Kikelj, D., Benek, O., Zega, A., Zidar, N., Ilas, J., Tomasic, T., Masic, L.P.
Funding Organization(s): Innovative Medicines Initiative, Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC), European Communitys Seventh Framework Programme, Slovenian Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.199 (Depositor), 0.203 (DCC)
R-Value Work:
0.142 (Depositor), 0.145 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

E.coli GyrB24 with inhibitor KOB20 (EBL2583)

Stevenson, C.E.M., Lawson, D.M., Maxwell, A.M., Henderson, S.R., Kikelj, D., Benek, O., Zega, A., Zidar, N., Ilas, J., Tomasic, T., Masic, L.P.

To be published.

Macromolecule Content

Total Structure Weight: 24.82 kDa
Atom Count: 1,758
Modeled Residue Count: 195
Deposited Residue Count: 220
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A	220	Escherichia coli K-12	Mutation(s): 0 Gene Names: gyrB, acrB, cou, himB, hisU, nalC, parA, pcbA, b3699, JW5625 EC: 5.6.2.2
UniProt
Find proteins for P0AES6 (Escherichia coli (strain K12)) Explore P0AES6 Go to UniProtKB: P0AES6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AES6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4Q6 (Subject of Investigation/LOI) Query on 4Q6 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2Z)-2-[[4,5-bis(bromanyl)-1H-pyrrol-2-yl]carbonylimino]-3-(phenylmethyl)-1,3-benzothiazole-6-carboxylic acid C₂₀ H₁₃ Br₂ N₃ O₃ S BDKGNCMGGSFVCT-GFMRDNFCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.199 (Depositor), 0.203 (DCC)
R-Value Work: 0.142 (Depositor), 0.145 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.17	α = 90
b = 49.77	β = 102.11
c = 53.04	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Innovative Medicines Initiative	European Union	Grant No. 115583
Wellcome Trust	United Kingdom	110072/Z/15/Z
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BBSRC Institute Strategic Programme Grant
European Communitys Seventh Framework Programme	European Union	(FP7/2007-2013)
Slovenian Research Agency	European Union	P1-0208