PDB-8j9t: Crystal Structure of GyraseA N-terminal at 2.43A Resolution

ID or keywords:

Entry

Database: PDB / ID: 8j9t

Title

Crystal Structure of GyraseA N-terminal at 2.43A Resolution

Components

DNA gyrase subunit A

Keywords

ISOMERASE / Gyrase / GANTD / Salmonella

Function / homology

Function and homology information

DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / cytoplasm
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.428 Å

Authors

Salman, M. / Sachdeva, E. / Das, U. / Singh, T.P. / Ethayathullah, A.S. / Kaur, P.

Funding support

1items

Citation

Journal: to be published
Title: Crystal Structure of GyraseA N-terminal at 2.43A Resolution
Authors: Salman, M. / Sachdeva, E. / Das, U. / Singh, T.P. / Ethayathullah, A.S. / Kaur, P.

History

Deposition	May 4, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8j9t.cif.gz	348.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8j9t.ent.gz	250.1 KB	Display	PDB format
PDBx/mmJSON format	8j9t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8j9t_validation.pdf.gz	449.9 KB	Display	wwPDB validaton report
Full document	8j9t_full_validation.pdf.gz	456 KB	Display
Data in XML	8j9t_validation.xml.gz	40.9 KB	Display
Data in CIF	8j9t_validation.cif.gz	59.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j9/8j9t ftp://data.pdbj.org/pub/pdb/validation_reports/j9/8j9t	HTTPS FTP

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Related structure data

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	#73 - Jan 2006 Topoisomerase similarity (7) #131 - Nov 2010 Inteins similarity (6) #193 - Jan 2016 Siderocalin similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #35 - Nov 2002 Ferritin and Transferrin similarity (1) #37 - Jan 2003 Serum Albumin similarity (1)

Deposited unit

A: DNA gyrase subunit A

B: DNA gyrase subunit A

hetero molecules

111 kDa, 2 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)	154.781, 154.781, 108.258
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	DNA gyrase subunit A Mass: 55373.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) Gene: gyrA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A716CHN5
#2: Chemical	ChemComp-CO3 / CARBONATE ION Mass: 60.009 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CO₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.41 Å³/Da / Density % sol: 63.96 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3500, Tris

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 1, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8731 Å / Relative weight: 1
Reflection	Resolution: 2.42→134.04 Å / Num. obs: 55446 / % possible obs: 99.1 % / Redundancy: 10.1 % / CC_1/2: 0.993 / Net I/σ(I): 8.8
Reflection shell	Resolution: 2.42→2.49 Å / Num. unique obs: 4093 / CC_1/2: 0.375

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing
MxCuBE		data collection
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.428→45.93 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.931 / WR_factor R_free: 0.219 / WR_factor R_work: 0.185 / Average fsc free: 0.9592 / Average fsc work: 0.97 / Cross valid method: FREE R-VALUE / ESU R Free: 0.229
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2348	2005	3.632 %
R_work	0.1993	53201	-
all	0.201	-	-
obs	-	55206	99.062 %

Solvent computation

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

Displacement parameters

B_iso mean: 51.717 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.037 Å²	0.018 Å²	0 Å²
2-	-	0.037 Å²	-0 Å²
3-	-	-	-0.119 Å²

Refinement step

Cycle: LAST / Resolution: 2.428→45.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7702	0	8	627	8337

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	7830
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7672
X-RAY DIFFRACTION	r_angle_refined_deg	1.29	1.65	10582
X-RAY DIFFRACTION	r_angle_other_deg	0.623	1.574	17610
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.227	5	970
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.649	5	80
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.387	10	1424
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.694	10	382
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	1196
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	9320
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1760
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	1569
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.221	0.2	7035
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	3919
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	4592
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	312
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.06	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.285	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.26	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.397	0.2	6
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.386	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0	5.486	3892
X-RAY DIFFRACTION	r_mcbond_other	0	5.486	3892
X-RAY DIFFRACTION	r_mcangle_it	0	9.84	4858
X-RAY DIFFRACTION	r_mcangle_other	0	9.841	4859
X-RAY DIFFRACTION	r_scbond_it	0	5.806	3938
X-RAY DIFFRACTION	r_scbond_other	0	5.807	3936
X-RAY DIFFRACTION	r_scangle_it	0	10.461	5724
X-RAY DIFFRACTION	r_scangle_other	0	10.463	5722
X-RAY DIFFRACTION	r_lrange_it	0	53.503	8683
X-RAY DIFFRACTION	r_lrange_other	0	53.424	8611
X-RAY DIFFRACTION	r_rigid_bond_restr	4.527	3	15502

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
2.428-2.491	0.379	130	0.348	3506	0.349	4109	0.915	0.936	88.4887	0.334
2.491-2.559	0.301	145	0.312	3838	0.311	3989	0.944	0.948	99.8496	0.292
2.559-2.632	0.311	140	0.306	3734	0.306	3876	0.953	0.951	99.9484	0.281
2.632-2.713	0.291	139	0.272	3631	0.273	3775	0.949	0.959	99.8676	0.246
2.713-2.802	0.308	129	0.255	3510	0.257	3640	0.942	0.962	99.9725	0.226
2.802-2.9	0.277	131	0.227	3401	0.229	3535	0.953	0.967	99.9151	0.2
2.9-3.009	0.255	126	0.209	3306	0.211	3435	0.961	0.972	99.9127	0.186
3.009-3.131	0.264	121	0.212	3141	0.214	3267	0.952	0.973	99.847	0.194
3.131-3.27	0.23	117	0.206	3049	0.207	3167	0.969	0.977	99.9684	0.192
3.27-3.428	0.228	108	0.217	2905	0.217	3014	0.974	0.979	99.9668	0.206
3.428-3.613	0.286	103	0.215	2773	0.217	2876	0.958	0.981	100	0.206
3.613-3.83	0.222	95	0.196	2626	0.197	2721	0.972	0.983	100	0.187
3.83-4.093	0.238	95	0.176	2472	0.178	2569	0.976	0.985	99.9221	0.17
4.093-4.418	0.202	83	0.149	2304	0.151	2387	0.978	0.987	100	0.148
4.418-4.835	0.168	83	0.131	2131	0.132	2214	0.984	0.99	100	0.132
4.835-5.398	0.195	74	0.168	1911	0.169	1985	0.98	0.987	100	0.167
5.398-6.219	0.248	67	0.205	1702	0.206	1769	0.973	0.984	100	0.206
6.219-7.582	0.167	51	0.191	1459	0.19	1510	0.983	0.984	100	0.196
7.582-10.58	0.188	42	0.127	1140	0.129	1183	0.98	0.991	99.9155	0.142
10.58-45.93	0.19	26	0.188	662	0.188	699	0.973	0.977	98.4263	0.215

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