PDB-8bp2: 2.8A STRUCTURE OF ZOLIFLODACIN WITH S.AUREUS DNA GYRASE AND DNA

ID or keywords:

Entry

Database: PDB / ID: 8bp2

Title

2.8A STRUCTURE OF ZOLIFLODACIN WITH S.AUREUS DNA GYRASE AND DNA

Components

(DNA gyrase subunit ...) x 2
DNA (20-MER)

Keywords

ISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR

Function / homology

Function and homology information

DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.8 Å

Authors

Bax, B.D. / Morgan, H. / Warren, A.J.

Funding support

United Kingdom, 1items

Citation

Journal: Int J Mol Sci / Year: 2023
Title: A 2.8 angstrom Structure of Zoliflodacin in a DNA Cleavage Complex with Staphylococcus aureus DNA Gyrase.
Authors: Morgan, H. / Lipka-Lloyd, M. / Warren, A.J. / Hughes, N. / Holmes, J. / Burton, N.P. / Mahenthiralingam, E. / Bax, B.D.

History

Deposition	Nov 15, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 8, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bp2.cif.gz	568.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8bp2.ent.gz		Display	PDB format
PDBx/mmJSON format	8bp2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8bp2_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8bp2_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8bp2_validation.xml.gz	51.4 KB	Display
Data in CIF	8bp2_validation.cif.gz	71.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bp/8bp2 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/8bp2	HTTPS FTP

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Related structure data

Related structure data	5cdmS 5cdo S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (3) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #73 - Jan 2006 Topoisomerase similarity (22) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #131 - Nov 2010 Inteins similarity (7) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Deposited unit

BBB: DNA gyrase subunit B

AAA: DNA gyrase subunit A

DDD: DNA gyrase subunit B

CCC: DNA gyrase subunit A

EEE: DNA (20-MER)

EbE: DNA (20-MER)

FFF: DNA (20-MER)

FbF: DNA (20-MER)

hetero molecules

180 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	94.542, 94.542, 417.134
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

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DNA gyrase subunit ... , 2 types, 4 molecules BBBDDDAAACCC

#1: Protein	DNA gyrase subunit B Mass: 21274.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli) References: UniProt: P66937, DNA topoisomerase (ATP-hydrolysing)
#2: Protein	DNA gyrase subunit A Mass: 55537.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) References: UniProt: Q99XG5, DNA topoisomerase (ATP-hydrolysing)

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DNA chain , 1 types, 4 molecules EEEEbEFFFFbF

#3: DNA chain	DNA (20-MER) Mass: 6150.966 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 241 molecules

#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#8: Chemical	ChemComp-R8U / Zoliflodacin / (4'~{R},6'~{S},7'~{S})-17'-fluoranyl-4',6'-dimethyl-13'-[(4~{S})-4-methyl-2-oxidanylidene-1,3-oxazolidin-3-yl]spiro[1,3-diazinane-5,8'-5,15-dioxa-2,14-diazatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(17),10,12(16),13-tetraene]-2,4,6-trione Mass: 487.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₂H₂₂FN₅O₇ / Feature type: SUBJECT OF INVESTIGATION
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.28 Å³/Da / Density % sol: 62.51 %
Crystal grow	Temperature: 293 K / Method: batch mode / pH: 6.3 / Details: 90 mM bistris pH 6.3, 9% PEG 5000MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 8, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 2.78→25 Å / Num. obs: 52704 / % possible obs: 100 % / Redundancy: 18.5 % / CC_1/2: 0.997 / Net I/σ(I): 5.9
Reflection shell	Resolution: 2.78→2.83 Å / Num. unique obs: 2554 / CC_1/2: 0.318

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DIALS		data reduction
DIALS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 5CDM

5cdm

Resolution: 2.8→24.854 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.941 / SU B: 44.615 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R: 1.443 / ESU R Free: 0.324 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2314	2538	4.945 %
R_work	0.1908	48785	-
all	0.193	-	-
obs	-	51323	99.405 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 92.396 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.23 Å²	1.115 Å²	0 Å²
2-	-	2.23 Å²	-0 Å²
3-	-	-	-7.233 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→24.854 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10545	801	130	227	11703

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	11815
X-RAY DIFFRACTION	r_angle_refined_deg	1.722	1.671	16137
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.768	5	1343
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.114	21.151	643
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.392	15	1968
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.035	15	117
X-RAY DIFFRACTION	r_chiral_restr	0.114	0.2	1602
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	8603
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	5458
X-RAY DIFFRACTION	r_nbtor_refined	0.32	0.2	7980
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.18	0.2	504
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.253	0.2	40
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.167	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.817	3.569	5375
X-RAY DIFFRACTION	r_mcangle_it	3.131	5.365	6734
X-RAY DIFFRACTION	r_scbond_it	2.739	3.922	6440
X-RAY DIFFRACTION	r_scangle_it	4.387	5.806	9403
X-RAY DIFFRACTION	r_lrange_it	12.356	70.624	51565

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.8-2.872	0.385	185	0.366	3421	0.367	3812	0.522	0.543	94.596	0.364
2.872-2.949	0.354	188	0.356	3460	0.356	3672	0.592	0.594	99.3464	0.356
2.949-3.034	0.388	162	0.351	3385	0.353	3548	0.524	0.553	99.9718	0.35
3.034-3.126	0.341	153	0.336	3291	0.336	3444	0.596	0.652	100	0.337
3.126-3.226	0.341	163	0.322	3206	0.323	3369	0.737	0.697	100	0.323
3.226-3.338	0.298	166	0.28	3108	0.281	3274	0.751	0.8	100	0.279
3.338-3.461	0.285	175	0.25	2959	0.252	3134	0.843	0.851	100	0.242
3.461-3.6	0.27	126	0.214	2903	0.216	3029	0.858	0.898	100	0.2
3.6-3.756	0.24	154	0.204	2768	0.206	2922	0.904	0.925	100	0.188
3.756-3.935	0.211	115	0.166	2689	0.168	2804	0.939	0.947	100	0.147
3.935-4.142	0.179	141	0.153	2479	0.155	2620	0.955	0.959	100	0.131
4.142-4.386	0.174	153	0.137	2360	0.139	2513	0.955	0.963	100	0.119
4.386-4.678	0.17	117	0.124	2254	0.126	2371	0.958	0.969	100	0.107
4.678-5.038	0.166	86	0.131	2117	0.132	2203	0.955	0.965	100	0.112
5.038-5.496	0.234	99	0.157	1944	0.161	2043	0.915	0.948	100	0.138
5.496-6.108	0.248	97	0.189	1754	0.192	1851	0.915	0.934	100	0.167
6.108-6.983	0.287	71	0.191	1582	0.195	1653	0.902	0.939	100	0.173
6.983-8.388	0.187	72	0.146	1340	0.148	1412	0.953	0.961	100	0.133
8.388-11.24	0.166	71	0.123	1051	0.125	1122	0.969	0.976	100	0.124
11.24-24.854	0.208	44	0.149	700	0.152	744	0.957	0.966	100	0.161

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.4507	0.9094	-0.9956	3.0403	-1.8804	1.5177	-0.0176	-0.6226	0.1913	0.6662	0.1701	0.4238	-0.5041	-0.443	-0.1524	1.3032	0.0167	0.1912	0.6995	-0.0871	0.8064	14.7529	52.4628	64.1285
2	1.9714	0.149	-0.0974	3.1056	0.4646	2.1337	0.0328	0.1473	-0.2267	0.4632	-0.166	0.054	-0.0171	0.0703	0.1332	0.4926	-0.1463	0.1019	0.0608	-0.015	0.7182	29.0477	27.6594	33.7295
3	8.1535	7.8367	1.7159	9.884	-0.19	1.8078	0.2673	0.5068	-0.7325	0.3278	-0.0459	-0.6734	0.06	0.516	-0.2214	0.6369	-0.0363	0.0212	0.1659	0.0076	0.84	27.9386	-4.4252	38.0777
4	8.4207	-0.0426	1.7102	2.807	-0.8859	0.6457	-0.071	-0.181	-0.3347	-0.1015	0.0845	-0.0408	0.1424	-0.1048	-0.0135	0.8139	-0.131	0.0079	0.2043	-0.0117	0.7004	10.8626	-16.2515	45.2152
5	3.1734	-1.5861	-1.4166	3.0489	4.3237	6.6896	-0.5537	-0.9834	-0.0374	0.4237	0.5097	-0.0797	-0.0354	0.6131	0.0441	1.2596	-0.1218	-0.0743	0.5443	0.0316	0.7826	34.3078	45.4618	61.0765
6	5.0182	-0.6353	-0.6292	1.0158	0.1988	2.4415	0.0123	0.61	0.2908	-0.3828	0.0748	-0.2378	-0.5685	0.4148	-0.087	1.0552	-0.06	0.1717	0.6109	0.1282	0.8504	-3.5347	51.8629	16.3302
7	1.7752	-0.0371	-0.9538	3.1636	-0.6627	2.5197	0.0012	0.0173	-0.3005	-0.1594	-0.2026	-0.0346	0.1155	-0.053	0.2014	0.2913	-0.0295	0.0422	0.05	0.0297	0.7272	-20.4734	30.9031	47.8874
8	3.8052	-5.3	-1.5866	11.6658	2.7559	0.7374	0.1184	-0.1764	-0.1228	-0.0647	-0.118	0.0952	-0.0826	0.0125	-0.0005	0.7405	-0.0684	0.044	0.2144	0.0053	0.839	-21.5112	-1.4182	45.8161
9	9.1616	-2.1589	-0.1196	1.5371	1.3544	2.0181	-0.1592	0.2786	-0.1292	0.0184	0.0196	0.0491	0.0349	0.2241	0.1396	0.7633	-0.1781	0.019	0.1096	0.045	0.6816	-5.6747	-15.2084	39.4922
10	3.0261	1.2183	0.4098	1.9791	-2.7327	6.6777	-0.4295	0.9418	-0.0436	-0.4411	0.4194	0.1083	-0.0415	-0.6794	0.0101	1.094	0.1565	-0.0285	0.8623	-0.0444	0.8194	-23.531	46.7297	19.2412
11	4.2663	-0.3016	0.1985	1.3473	-0.1312	5.9883	-0.5334	0.4561	0.564	0.2718	0.0664	0.0617	-0.7273	-0.8762	0.4669	0.7396	-0.1394	0.1384	0.2655	-0.0376	0.7722	23.2614	48.7735	41.2006
12	7.2225	0.1688	3.2332	1.9493	0.0063	6.9838	-0.5094	-0.742	0.7154	-0.2121	0.2376	0.0204	-0.5737	0.1394	0.2717	0.6139	0.0659	0.1542	0.1726	0.0307	0.6977	-12.9799	50.4487	39.2643
13	2.1581	0.1693	-0.1244	2.8484	-2.7799	5.4032	-0.1131	0.5004	0.4393	0.6366	0.0307	0.2919	-1.1511	-0.3321	0.0824	0.7663	-0.2299	0.0276	0.3156	-0.0264	0.754	29.2339	55.0909	13.9245
14	2.5737	1.013	-0.8464	3.8938	1.6113	4.1924	-0.4409	-0.2489	0.3668	-0.1125	0.2959	-0.4429	-0.5838	0.5457	0.145	0.7272	0.0523	-0.1535	0.2035	0.0619	0.8505	-17.9961	59.609	65.7469

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	B - BBB	419 - 608
2	X-RAY DIFFRACTION	2	ALL	A - AAA	29 - 244
3	X-RAY DIFFRACTION	2	ALL	A - AAA	328 - 369
4	X-RAY DIFFRACTION	2	ALL	A - AAA	461 - 489
5	X-RAY DIFFRACTION	3	ALL	A - AAA	370 - 379
6	X-RAY DIFFRACTION	3	ALL	A - AAA	445 - 460
7	X-RAY DIFFRACTION	4	ALL	A - AAA	380 - 444
8	X-RAY DIFFRACTION	5	ALL	A - AAA	11 - 28
9	X-RAY DIFFRACTION	5	ALL	B - BBB	609 - 638
10	X-RAY DIFFRACTION	6	ALL	D - DDD	419 - 608
11	X-RAY DIFFRACTION	7	ALL	C - CCC	29 - 244
12	X-RAY DIFFRACTION	7	ALL	C - CCC	328 - 369
13	X-RAY DIFFRACTION	7	ALL	C - CCC	461 - 490
14	X-RAY DIFFRACTION	8	ALL	C - CCC	370 - 379
15	X-RAY DIFFRACTION	8	ALL	C - CCC	445 - 460
16	X-RAY DIFFRACTION	9	ALL	C - CCC	380 - 444
17	X-RAY DIFFRACTION	10	ALL	C - CCC	10 - 28
18	X-RAY DIFFRACTION	10	ALL	D - DDD	609 - 639
19	X-RAY DIFFRACTION	11	ALL	E - EEE	2 - 8
20	X-RAY DIFFRACTION	11	ALL	F - FbF	2010 - 2019
21	X-RAY DIFFRACTION	12	ALL	E - EbE	2010 - 2019
22	X-RAY DIFFRACTION	12	ALL	F - FFF	2 - 8
23	X-RAY DIFFRACTION	13	ALL	A - AAA	245 - 327
24	X-RAY DIFFRACTION	14	ALL	C - CCC	245 - 327

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DNA gyrase subunit ... , 2 types, 4 molecules BBBDDDAAACCC

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