PDB-4ckk: Apo structure of 55 kDa N-terminal domain of E. coli DNA gyrase A...

ID or keywords:

Entry

Database: PDB / ID: 4ckk

Title

Apo structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit

Components

DNA GYRASE SUBUNIT A

Keywords

ISOMERASE / DNA GYRASE / TOPOISOMERASE / ANTIBIOTIC TARGET

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 / cytoplasm
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Hearnshaw, S.J. / Edwards, M.J. / Stevenson, C.E.M. / Lawson, D.M. / Maxwell, A.

Citation

Journal: J.Mol.Biol. / Year: 2014
Title: A New Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8 Bound to DNA Gyrase Gives Fresh Insight Into the Mechanism of Inhibition.
Authors: Hearnshaw, S.J. / Edwards, M.J. / Stevenson, C.E. / Lawson, D.M. / Maxwell, A.

History

Deposition	Jan 7, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 19, 2014	Group: Database references
Revision 1.2	May 14, 2014	Group: Database references
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ckk.cif.gz	761.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ckk.ent.gz	633.7 KB	Display	PDB format
PDBx/mmJSON format	4ckk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ckk_validation.pdf.gz	437.8 KB	Display	wwPDB validaton report
Full document	4ckk_full_validation.pdf.gz	444.5 KB	Display
Data in XML	4ckk_validation.xml.gz	73.5 KB	Display
Data in CIF	4ckk_validation.cif.gz	106 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ck/4ckk ftp://data.pdbj.org/pub/pdb/validation_reports/ck/4ckk	HTTPS FTP

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Related structure data

Related structure data	4cklC 2y3pS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2y3p-d 3ilw-d 6bq9-1 1ab4-1 2fh4-d 3lpx-d 4ckl-2 2inr-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#73 - Jan 2006 Topoisomerase similarity (8) #131 - Nov 2010 Inteins similarity (6)

Deposited unit

A: DNA GYRASE SUBUNIT A

B: DNA GYRASE SUBUNIT A

C: DNA GYRASE SUBUNIT A

D: DNA GYRASE SUBUNIT A

222 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DNA GYRASE SUBUNIT A

C: DNA GYRASE SUBUNIT A

defined by author&software
111 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DNA GYRASE SUBUNIT A

D: DNA GYRASE SUBUNIT A

defined by author&software
111 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.570, 95.530, 95.890
Angle α, β, γ (deg.)	105.16, 118.81, 103.42
Int Tables number	1
Space group name H-M	P1

#1: Protein	DNA GYRASE SUBUNIT A Mass: 55381.398 Da / Num. of mol.: 4 / Fragment: 55 KDA N-TERMINAL DOMAIN, RESIDUES 30-522 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: JMTACA / Plasmid: PRJR10.18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B843 / Variant (production host): PLYSS References: UniProt: P0AES5, UniProt: A0A0H3JH39*PLUS, EC: 5.99.1.3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1056 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

DNA GYRASE SUBUNIT A

Mass: 55381.398 Da / Num. of mol.: 4 / Fragment: 55 KDA N-TERMINAL DOMAIN, RESIDUES 30-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

ESCHERICHIA COLI (E. coli) / Strain: JMTACA / Plasmid: PRJR10.18 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): B843 / Variant (production host): PLYSS
References: UniProt: P0AES5, UniProt: A0A0H3JH39*PLUS, EC: 5.99.1.3

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1056 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 59 % / Description: NONE
Crystal grow	pH: 8.5 / Details: pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9686 Å / Relative weight: 1
Reflection	Resolution: 1.9→81.51 Å / Num. obs: 194509 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / B_iso Wilson estimate: 23.6 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 11
Reflection shell	Resolution: 1.9→1.95 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / % possible all: 94.7

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y3P

2y3p

Resolution: 1.9→81.51 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.956 / SU B: 4.872 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18859	9799	5 %	RANDOM
R_work	0.16935	-	-	-
obs	0.17031	184697	96.97 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 32.3 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.13 Å²	0.06 Å²	0.59 Å²
2-	-	0.22 Å²	0.4 Å²
3-	-	-	0.25 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→81.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15016	0	0	1056	16072

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	15297
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	14970
X-RAY DIFFRACTION	r_angle_refined_deg	1.502	1.971	20746
X-RAY DIFFRACTION	r_angle_other_deg	1.312	3	34241
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.218	5	1937
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.591	23.73	705
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.418	15	2661
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.352	15	141
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	2397
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	17363
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	3374
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.228	1.503	7748
X-RAY DIFFRACTION	r_mcbond_other	1.228	1.503	7747
X-RAY DIFFRACTION	r_mcangle_it	1.871	2.244	9670
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.244	1.806	7549
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.286	737	-
R_work	0.265	13410	-
obs	-	-	94.69 %

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	1.3584	-0.5932	-0.5916	1.5522	1.2306	1.4778	0.0636	0.0845	-0.0305	-0.002	-0.1283	0.1066	0.0648	-0.1641	0.0647	0.026	0.011	0.0119	0.058	0.0014	0.0414	-1.0344	1.8444	6.9127
2	2.5512	0.3606	1.683	1.7659	0.9674	3.1374	0.0189	0.0263	-0.0311	0.1382	0.097	-0.2826	0.0675	0.2931	-0.1159	0.068	0.0582	0.0064	0.0898	-0.006	0.116	25.8682	-7.9245	13.1143
3	4.2357	-3.1218	2.4532	2.4267	-1.8255	1.4354	0.0405	0.0756	-0.1974	-0.0295	0.046	0.1823	0.002	-0.0045	-0.0865	0.1326	0.0302	-0.0183	0.1972	-0.0591	0.0963	-13.7518	-0.5878	-10.9007
4	6.7418	-0.1395	-1.2721	3.8685	2.8107	8.0896	0.2748	-0.0856	0.455	-0.2352	-0.2156	0.0036	-0.4881	0.0988	-0.0592	0.1165	0.0106	-0.0564	0.1308	-0.0112	0.0993	-38.3689	18.8501	-21.7896
5	4.1364	-3.3623	-0.5064	3.0229	1.0557	2.3577	0.2139	0.1985	0.0448	-0.3117	0.0144	-0.1884	-0.0892	0.4471	-0.2284	0.2118	-0.0546	0.0227	0.2987	-0.0347	0.2012	-25.2635	11.8949	-21.8502
6	8.583	-0.8769	5.5543	1.6297	-0.0173	6.2311	0.1701	0.8548	-0.091	-0.2788	-0.23	0.0078	-0.0348	0.1807	0.0599	0.108	0.0758	0.0511	0.1937	-0.0203	0.0698	7.5815	-2.6124	-10.8502
7	0.931	0.9252	0.0184	1.6707	0.4355	0.5843	-0.029	-0.0095	-0.0014	0.0465	-0.025	0.0634	0.069	-0.0257	0.0541	0.0599	0.0066	-0.0269	0.036	-0.0048	0.0482	-25.0784	-33.2133	37.7371
8	1.7551	0.3279	-0.6525	1.2712	-0.6844	4.2188	0.0564	-0.4362	0.0509	0.3621	-0.0429	0.0294	-0.0986	0.1194	-0.0135	0.1663	-0.0107	-0.0625	0.1371	-0.0285	0.1071	-11.8926	-21.8836	61.632
9	4.3333	-0.7788	4.7624	0.3962	-0.378	6.2952	0.1792	0.2678	-0.1084	-0.0632	-0.0261	-0.0368	0.238	0.2893	-0.1531	0.1246	-0.0608	-0.0035	0.0677	0.0158	0.086	-17.2848	-25.9333	22.4075
10	6.2299	1.7997	-0.6022	3.4268	1.0085	4.0361	-0.2021	0.1485	0.2583	0.0218	0.114	0.2053	-0.1277	0.0972	0.0881	0.1068	0.0528	-0.0362	0.1197	-0.0051	0.0268	-48.758	-28.012	-6.1187
11	3.8566	1.4496	2.3756	1.1463	0.9224	1.5659	-0.0714	0.2726	0.3063	-0.0432	-0.0917	0.0485	-0.1987	0.2083	0.1631	0.2696	-0.0191	-0.0097	0.1959	-0.0149	0.119	-38.8095	-22.3863	2.0188
12	1.375	0.2224	0.6189	1.0961	-0.0246	10.4392	-0.1581	0.143	0.2333	-0.1091	0.0544	0.033	-0.5492	0.0474	0.1037	0.1121	-0.0238	-0.0765	0.0194	0.0154	0.133	-19.9029	-14.119	32.8604
13	1.2846	-0.2272	-0.7245	2.4687	0.4802	1.2154	-0.0329	0.0082	0.0225	-0.0951	0.0217	-0.1446	0.0519	0.0317	0.0112	0.0084	0.0004	0.0107	0.0459	-0.0197	0.0388	-20.8654	16.0412	27.5284
14	0.9629	-0.6325	0.5166	2.8607	-1.3536	1.7961	-0.0617	-0.1588	-0.1223	0.2849	0.0764	0.0246	0.0973	0.052	-0.0147	0.0773	0.0349	0.0076	0.1306	-0.0229	0.0421	-26.5057	11.2572	55.0717
15	1.0179	-0.4954	2.1376	1.3404	-1.9364	7.6432	-0.0105	0.1239	0.0628	-0.0829	-0.041	-0.1644	-0.1187	0.3256	0.0514	0.0256	-0.0001	0.0214	0.042	-0.0223	0.062	-26.249	35.629	25.2617
16	7.2948	-2.094	-4.2527	6.6906	2.954	5.9948	0.0895	0.2659	0.0592	-0.9784	-0.0015	-0.2255	-1.0136	-0.2579	-0.0881	0.5889	-0.0461	0.0096	0.2329	0.065	0.0887	-30.8718	39.5369	-15.0009
17	2.6279	0.5725	-0.3232	2.6359	3.1121	5.7487	0.0582	0.1296	0.1851	-0.5211	-0.1289	0.1189	-0.8939	-0.2714	0.0706	0.3724	0.0178	-0.0337	0.2025	0.017	0.1255	-34.4394	39.2934	-3.3242
18	0.4127	-0.9157	0.5693	5.439	-4.5528	4.4987	0.0436	-0.0161	0.0304	-0.0787	0.0866	0.135	-0.0514	-0.1486	-0.1302	0.0271	0.0121	0.0146	0.0891	-0.0364	0.0657	-37.8944	32.0614	30.7603
19	3.2259	1.2128	-0.035	1.8518	0.3825	0.4397	0.0552	-0.155	0.0572	0.1858	-0.0331	-0.0412	0.0227	-0.0253	-0.0221	0.066	-0.0074	-0.0201	0.0362	0.001	0.049	-42.392	-60.2811	35.0443
20	3.8197	-0.4145	1.4021	1.923	-0.0808	2.1734	-0.0171	-0.4147	-0.4935	0.5201	0.0893	0.1317	0.2537	-0.2038	-0.0723	0.2158	-0.0176	0.0142	0.0683	0.0571	0.1113	-55.3764	-81.5304	39.0098
21	4.1002	-2.0659	1.5146	2.6076	-0.3697	2.5644	-0.0026	0.0555	-0.2575	0.1579	-0.0142	-0.263	0.1538	0.2031	0.0168	0.2546	0.0007	-0.1079	0.1365	0.0517	0.34	-28.927	-92.1206	44.233
22	0.2142	-0.3093	-0.022	3.0092	-1.46	1.0854	0.0327	-0.047	0.0245	0.2579	-0.0181	0.0991	-0.2085	-0.0383	-0.0146	0.058	-0.0065	-0.005	0.0946	-0.024	0.1141	-62.6997	-51.3947	24.4948
23	1.728	-0.1893	-0.6772	3.5982	-0.6988	2.1231	-0.0569	0.0543	-0.2282	-0.0185	0.0826	0.4166	0.1998	-0.2474	-0.0256	0.1764	0.0531	-0.033	0.1362	-0.0106	0.1403	-68.3546	-38.0414	8.2676
24	5.6085	-4.2828	2.0054	5.5541	-1.6442	1.4909	0.1426	0.1815	-0.1651	-0.1921	-0.0502	0.3593	0.1333	-0.0765	-0.0925	0.0928	-0.0546	0.0032	0.0575	-0.0103	0.0898	-60.5694	-70.2871	23.9164

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	33 - 198
2	X-RAY DIFFRACTION	2	A	199 - 332
3	X-RAY DIFFRACTION	3	A	333 - 397
4	X-RAY DIFFRACTION	4	A	398 - 423
5	X-RAY DIFFRACTION	5	A	424 - 493
6	X-RAY DIFFRACTION	6	A	494 - 522
7	X-RAY DIFFRACTION	7	B	33 - 198
8	X-RAY DIFFRACTION	8	B	199 - 332
9	X-RAY DIFFRACTION	9	B	333 - 380
10	X-RAY DIFFRACTION	10	B	381 - 423
11	X-RAY DIFFRACTION	11	B	424 - 492
12	X-RAY DIFFRACTION	12	B	493 - 522
13	X-RAY DIFFRACTION	13	C	33 - 174
14	X-RAY DIFFRACTION	14	C	175 - 332
15	X-RAY DIFFRACTION	15	C	333 - 384
16	X-RAY DIFFRACTION	16	C	385 - 422
17	X-RAY DIFFRACTION	17	C	423 - 483
18	X-RAY DIFFRACTION	18	C	484 - 522
19	X-RAY DIFFRACTION	19	D	33 - 172
20	X-RAY DIFFRACTION	20	D	179 - 240
21	X-RAY DIFFRACTION	21	D	241 - 330
22	X-RAY DIFFRACTION	22	D	331 - 404
23	X-RAY DIFFRACTION	23	D	405 - 483
24	X-RAY DIFFRACTION	24	D	484 - 522

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