PDB-8tch: Initiation of replication protein with helicase activity encoded ...

ID or keywords:

Entry

Database: PDB / ID: 8tch

Title

Initiation of replication protein with helicase activity encoded by Pathogenicity Island SaPIBov1

Components

Pathogenicity island protein

Keywords

REPLICATION / initiator of replication with helicase activity / ATPase

Function / homology

Domain of unknown function DUF927 / Domain of unknown function (DUF927) / Pathogenicity island protein

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.7 Å

Authors

Mir-Sanchis, I. / Rice, P.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Initiation of replication protein with helicase activity encoded by Pathogenicity Island SaPIBov1
Authors: Mir-Sanchis, I. / Rice, P.

History

Deposition	Jul 1, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 3, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8tch.cif.gz	565.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8tch.ent.gz	480.5 KB	Display	PDB format
PDBx/mmJSON format	8tch.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8tch_validation.pdf.gz	449.5 KB	Display	wwPDB validaton report
Full document	8tch_full_validation.pdf.gz	468.8 KB	Display
Data in XML	8tch_validation.xml.gz	36 KB	Display
Data in CIF	8tch_validation.cif.gz	48.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tc/8tch ftp://data.pdbj.org/pub/pdb/validation_reports/tc/8tch	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15785/SBGRID/1033 / Data set type: diffraction image data / Details: Native dataset
Experimental dataset #2	Data reference: 10.15785/SBGRID/1034 / Data set type: diffraction image data / Details: SeMet dataset

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Pathogenicity island protein

B: Pathogenicity island protein

132 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pathogenicity island protein

B: Pathogenicity island protein

A: Pathogenicity island protein

B: Pathogenicity island protein

A: Pathogenicity island protein

B: Pathogenicity island protein

defined by author
Evidence: electron microscopy, hexamer
397 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	115.408, 115.408, 310.687
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	Pathogenicity island protein Mass: 66098.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: NCTC7878_00445 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2X2JYA8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.07 Å³/Da / Density % sol: 59.98 %
Crystal grow	Temperature: 288.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES, pH6,-25% Jeffermine M-600-12.5% Ethylene Glycol-5mM DTT

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 0.979415 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979415 Å / Relative weight: 1

Reflection

Resolution: 2.7→50 Å / Num. obs: 42298 / % possible obs: 99.7 % / Redundancy: 2.5 % / R_pim(I) all: 0.069 / R_rim(I) all: 0.157 / Χ²: 1.151 / Net I/σ(I): 4.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.7-2.75	2.5	1.058	2107	0.284	0.665	0.83	1.351	0.434	99.2
2.75-2.8	2.5	0.902	2103	0.409	0.762	0.698	1.145	0.446	99.4
2.8-2.85	2.4	0.754	2093	0.485	0.808	0.591	0.962	0.446	99
2.85-2.91	2.3	0.633	2086	0.54	0.837	0.503	0.812	0.457	98.8
2.91-2.97	2.5	0.547	2105	0.653	0.889	0.421	0.693	0.479	99.8
2.97-3.04	2.4	0.446	2120	0.709	0.911	0.348	0.568	0.513	99.6
3.04-3.12	2.5	0.385	2119	0.787	0.939	0.298	0.489	0.553	100
3.12-3.2	2.7	0.327	2110	0.835	0.954	0.246	0.411	0.635	100
3.2-3.3	2.6	0.27	2118	0.874	0.966	0.204	0.34	0.702	100
3.3-3.4	2.6	0.229	2116	0.914	0.977	0.171	0.287	0.878	100
3.4-3.52	2.6	0.197	2115	0.93	0.982	0.147	0.246	1.027	100
3.52-3.66	2.6	0.174	2090	0.93	0.982	0.128	0.217	1.317	99.8
3.66-3.83	2.6	0.15	2120	0.946	0.986	0.11	0.187	1.596	99.8
3.83-4.03	2.5	0.142	2079	0.934	0.983	0.106	0.178	2.048	99.4
4.03-4.29	2.3	0.132	2138	0.953	0.988	0.098	0.166	2.939	99.8
4.29-4.62	2.4	0.123	2113	0.959	0.989	0.09	0.153	3.249	99.9
4.62-5.08	2.7	0.111	2096	0.963	0.99	0.078	0.136	2.945	100
5.08-5.81	2.7	0.108	2138	0.969	0.992	0.076	0.132	2.666	99.6
5.81-7.32	2.5	0.105	2111	0.96	0.99	0.075	0.129	2.725	100
7.32-50	2.6	0.105	2110	0.966	0.991	0.069	0.126	6.479	99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
SOLVE		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.7→47.572 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 33.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2815	2076	4.91 %
R_work	0.2651	-	-
obs	0.2659	42298	99.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.7→47.572 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7865	0	0	38	7903

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8010
X-RAY DIFFRACTION	f_angle_d	0.707	10773
X-RAY DIFFRACTION	f_dihedral_angle_d	12.027	4844
X-RAY DIFFRACTION	f_chiral_restr	0.045	1196
X-RAY DIFFRACTION	f_plane_restr	0.004	1361

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.7003-2.7631	0.4054	132	0.3706	2645	X-RAY DIFFRACTION	98
2.7631-2.8322	0.3673	116	0.3601	2711	X-RAY DIFFRACTION	100
2.8322-2.9088	0.3208	124	0.3302	2692	X-RAY DIFFRACTION	100
2.9088-2.9943	0.3299	145	0.3202	2661	X-RAY DIFFRACTION	100
2.9943-3.091	0.3246	115	0.319	2716	X-RAY DIFFRACTION	100
3.091-3.2014	0.3681	153	0.3056	2692	X-RAY DIFFRACTION	100
3.2014-3.3296	0.3046	128	0.3072	2673	X-RAY DIFFRACTION	100
3.3296-3.4811	0.3232	120	0.3077	2699	X-RAY DIFFRACTION	100
3.4811-3.6645	0.3077	167	0.2916	2667	X-RAY DIFFRACTION	100
3.6645-3.894	0.296	152	0.2725	2649	X-RAY DIFFRACTION	100
3.894-4.1945	0.2908	169	0.2401	2668	X-RAY DIFFRACTION	100
4.1945-4.6163	0.2379	137	0.2237	2696	X-RAY DIFFRACTION	100
4.6163-5.2836	0.2465	127	0.2345	2695	X-RAY DIFFRACTION	100
5.2836-6.6538	0.2875	140	0.2643	2681	X-RAY DIFFRACTION	100
6.6538-47.572	0.2321	151	0.2329	2677	X-RAY DIFFRACTION	100

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	3.5599	-0.5545	-0.2572	3.3493	1.0094	2.4444	-0.0952	-0.326	-0.0999	0.3011	0.1271	0.0521	0.3304	0.0485	-0.0001	0.5812	-0.0373	-0.027	0.3749	0.1215	0.4438	50.5416	76.1949	217.4883
2	3.544	1.1425	-1.453	3.3172	-0.8322	8.4279	-0.4208	0.2344	0.1629	-0.1047	0.4679	0.2466	1.3855	-0.7052	0.0023	0.9245	-0.1708	0.0817	0.5005	0.1456	0.6517	59.2151	60.4821	178.3888
3	-2.0792	-0.876	-0.6364	-0.1591	-1.4925	1.2152	-0.1058	-0.0908	-0.0481	-0.8294	0.117	-0.0686	1.8535	0.0312	0.0159	1.4186	-0.0875	0.0631	0.7127	0.2214	0.8844	68.8552	61.5791	160.4715
4	3.6872	0.659	-0.5629	5.738	-0.8257	3.2547	-0.1024	0.2039	-0.4796	-0.1098	-0.2193	-0.5289	0.3258	0.2312	-0.0033	0.3767	0.0666	0.153	0.3993	0.0655	0.4624	75.4869	82.1272	137.7609
5	1.4212	0.6471	0.8189	1.8595	1.6089	3.315	0.1781	-0.0192	-0.0878	0.3384	-0.1724	0.1011	0.4079	-0.603	-0	0.4703	-0.0292	0.0611	0.6915	0.0626	0.5597	32.2574	90.4971	212.1966
6	3.6772	-0.2649	-1.2461	2.8451	0.9372	7.8324	0.1274	0.7079	0.049	-0.1978	-0.2004	-0.2419	0.2176	-1.5995	-0.0086	0.5484	-0.1375	0.2114	1.044	0.0194	0.7527	24.8885	77.3359	174.7949
7	4.4553	0.9831	-0.2939	0.1003	-0.0484	2.4292	-0.1475	-0.2264	-0.4081	0.0114	-0.0819	0.2189	0.277	-0.2917	-0.0054	0.5134	-0.0667	0.1406	0.3691	-0.0788	0.5861	44.1736	75.4615	142.7005

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 142 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 143 through 398 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 399 through 468 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 469 through 561 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 26 through 172 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 173 through 426 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 427 through 567 )

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