PDB-6h24: X-Ray Crystal Structure of the MSBI1.176 WH1 Domain, a Replicatio...

ID or keywords:

Entry

Database: PDB / ID: 6h24

Title

X-Ray Crystal Structure of the MSBI1.176 WH1 Domain, a Replication Protein Isolated from a Multiple Sclerosis Patient

Components

Replication protein

Keywords

REPLICATION / RepA / MSBI1.176 / WH1 / sclerosis

Function / homology

Initiator Rep protein / Initiator Replication protein, WH1 / Initiator Rep protein, WH2 / DNA replication initiation / DNA-directed DNA polymerase activity / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Replication protein

Function and homology information

Biological species

Sphinx1.76-related DNA (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.53 Å

Authors

Kilic, T. / Popov, A.N. / Hansman, G.S.

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structural analysis of a replication protein encoded by a plasmid isolated from a multiple sclerosis patient.
Authors: Kilic, T. / Popov, A.N. / Burk-Korner, A. / Koromyslova, A. / Zur Hausen, H. / Bund, T. / Hansman, G.S.

History

Deposition	Jul 13, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 15, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6h24.cif.gz	158.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6h24.ent.gz	128 KB	Display	PDB format
PDBx/mmJSON format	6h24.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h2/6h24 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/6h24	HTTPS FTP

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Related structure data

Similar structure data	1zg1-2 1je8-1 2z3r-6 2z3r-7 6ru4-2 5h5o-d 4l35-d 2z3r-2 6nwd-d 5ysc-d 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

Deposited unit

A: Replication protein

B: Replication protein

30.9 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)	32.380, 77.770, 47.680
Angle α, β, γ (deg.)	90.00, 90.66, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Replication protein Mass: 15454.439 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphinx1.76-related DNA (others) / Gene: Rep / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1T4J289
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 152 / 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: 1.94 Å³/Da / Density % sol: 36.64 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium acetate, 20% PEG3350

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N
3	100	1	N

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ESRF	ID23-1	1	1.85001
SYNCHROTRON	ESRF	ID23-1	2	0.972
SYNCHROTRON	ESRF	ID30B	3	0.97856

Detector

Type	ID	Detector	Date
DECTRIS PILATUS 6M	1	PIXEL	Dec 4, 2017
DECTRIS PILATUS 6M	2	PIXEL	Dec 4, 2017
DECTRIS PILATUS3 6M	3	PIXEL	May 12, 2018

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	MAD	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2
3	SINGLE WAVELENGTH	M	x-ray	3

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.85001	1
2	0.972	1
3	0.97856	1

Reflection

Resolution: 1.53→40.65 Å / Num. obs: 35709 / % possible obs: 99.42 % / Redundancy: 6.4 % / B_iso Wilson estimate: 22.19 Å² / CC_1/2: 1 / R_merge(I) obs: 0.04087 / R_pim(I) all: 0.0173 / R_rim(I) all: 0.04446 / Net I/σ(I): 20.91

Reflection shell

Resolution: 1.53→1.58 Å / R_merge(I) obs: 0.6848 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 3473 / CC_1/2: 0.85 / R_pim(I) all: 0.2973 / R_rim(I) all: 0.7487 / % possible all: 96.93

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS	VERSION Jan 26, 2018	data reduction
XSCALE	VERSION Jan 26, 2018	data scaling
HKL2Map		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.53→40.65 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.31

	R_factor	Num. reflection	% reflection
R_free	0.2116	1786	5 %
R_work	0.1855	-	-
obs	0.1868	35692	99.42 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.53→40.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2003	0	0	152	2155

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2066
X-RAY DIFFRACTION	f_angle_d	0.737	2822
X-RAY DIFFRACTION	f_dihedral_angle_d	11.607	1254
X-RAY DIFFRACTION	f_chiral_restr	0.046	335
X-RAY DIFFRACTION	f_plane_restr	0.005	367

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 (%)
1.5262-1.5675	0.285	132	0.2902	2496	X-RAY DIFFRACTION	96
1.5675-1.6136	0.2635	138	0.2461	2636	X-RAY DIFFRACTION	100
1.6136-1.6657	0.2536	136	0.2298	2583	X-RAY DIFFRACTION	100
1.6657-1.7252	0.2329	139	0.2198	2628	X-RAY DIFFRACTION	100
1.7252-1.7943	0.2557	138	0.2162	2613	X-RAY DIFFRACTION	100
1.7943-1.876	0.2305	135	0.2161	2564	X-RAY DIFFRACTION	99
1.876-1.9749	0.2702	138	0.1991	2624	X-RAY DIFFRACTION	100
1.9749-2.0986	0.1985	137	0.1887	2602	X-RAY DIFFRACTION	100
2.0986-2.2606	0.1819	137	0.1827	2610	X-RAY DIFFRACTION	100
2.2606-2.4881	0.1973	140	0.184	2648	X-RAY DIFFRACTION	100
2.4881-2.848	0.2173	137	0.1869	2602	X-RAY DIFFRACTION	100
2.848-3.5879	0.1998	139	0.1827	2649	X-RAY DIFFRACTION	100
3.5879-40.6611	0.205	140	0.1616	2651	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	7.698	6.1832	-5.841	5.0606	-4.8713	4.7578	0.3242	-0.4635	0.4589	0.2866	-0.2834	0.8942	0.0471	-0.2192	-0.1258	0.2937	-0.0061	0.0261	0.3466	-0.0279	0.3656	-6.0539	10.4122	22.4413
2	6.1646	3.7177	5.7544	4.434	4.2433	8.7487	-0.1888	0.4292	0.2474	-0.1935	0.0693	0.3011	-0.1187	0.0932	0.1302	0.1733	0.0039	0.0053	0.2163	0.0317	0.2578	-3.1441	16.7161	5.5929
3	5.2308	1.2378	3.0099	3.9134	-1.6019	3.2895	0.1418	0.2937	-0.1252	-0.1707	-0.0717	-0.2661	0.1931	-0.1562	-0.0625	0.2032	-0.0033	0.0178	0.2898	-0.0284	0.2717	-3.679	3.3406	1.5937
4	1.9933	-1.0733	-0.297	5.0829	-0.564	1.9936	0.0841	0.6313	0.6734	-0.5931	-0.0834	0.3332	-0.2126	-0.3864	-0.1617	0.1751	0.0206	-0.0099	0.3661	0.1196	0.3504	-1.4493	19.857	-1.2783
5	3.0652	2.6836	-4.0791	5.9384	-2.4509	7.7978	0.0752	0.1003	0.8969	0.0684	-0.2529	0.4436	-0.5132	-0.3568	-0.0987	0.5151	0.0138	0.1098	0.3243	0.1267	0.7166	4.8586	29.0752	-0.7392
6	1.5268	0.0638	-0.4142	1.8606	-2.6111	3.9387	0.0008	0.4127	0.4693	-0.0516	-0.0671	-0.3555	-0.4033	0.1659	0.0476	0.2399	0.0024	0.0097	0.282	0.0477	0.3835	8.6223	17.4829	5.8718
7	4.0114	2.053	-1.221	5.6229	-2.6402	3.7469	0.2361	-0.4324	-0.3797	0.5952	-0.1895	0.1329	-0.1882	-0.1512	-0.0635	0.1976	0.0037	-0.0127	0.2196	0.0134	0.2519	0.4631	3.8377	22.7263
8	1.7935	1.3399	2.4514	1.2435	2.1637	3.8111	0.2094	-0.5151	-0.4225	0.6282	-0.1907	-0.016	0.4097	0.0028	0.0664	0.2751	0.0101	0.0323	0.3109	0.0663	0.2962	-0.4528	-3.6282	26.0406
9	2.0856	0.2984	-0.2105	2.0061	-1.5233	2.5741	0.0766	0.4089	0.2488	-0.1458	-0.0102	0.0074	-0.1404	0.0663	0.0139	0.1887	-0.001	-0.0015	0.2294	0.0314	0.2484	6.3024	10.3176	3.0717
10	3.8096	-3.872	1.4638	9.1088	-1.3622	2.0352	-0.169	-0.1344	0.1021	0.2281	0.0568	0.4058	-0.1878	-0.1882	0.0827	0.2076	0.0077	0.0068	0.265	-0.0033	0.3152	-8.6708	13.3862	12.6744
11	3.223	-0.9732	0.9962	5.7163	-6.4455	7.2916	0.0597	0.151	-0.2912	-0.5068	-0.3461	-0.3364	0.5301	0.4418	0.2235	0.2313	0.0224	0.0398	0.231	-0.0148	0.2894	20.473	-3.0259	5.5704
12	1.1053	-0.102	0.6496	2.4499	-2.0002	2.7408	0.0415	-0.1519	-0.226	-0.0325	-0.0698	0.0031	0.1285	0.0671	0.0681	0.1666	0.0122	0.0027	0.1881	0.0155	0.2736	13.097	-8.5084	19.3232
13	2.3976	0.0261	-0.2405	8.0624	-5.5453	3.9057	0.0492	0.1934	0.0115	-0.7741	-0.072	-0.0639	0.6886	0.0734	0.0226	0.1923	0.0003	-0.0062	0.197	-0.0095	0.2265	12.0519	5.9131	0.3009
14	2.6739	-0.3975	0.4284	5.1907	-3.8893	9.2443	-0.0276	-0.4138	-0.3227	0.2702	0.1928	0.1889	-0.0271	-0.4161	-0.2093	0.1437	-0.019	-0.0043	0.2338	0.0592	0.2557	5.1391	-5.4484	23.3157
15	3.0485	-2.8622	2.2384	5.7484	-1.3804	5.9536	0.2346	0.0826	-0.2725	-0.0904	-0.0105	0.0186	0.4219	0.4599	-0.255	0.2637	0.0021	-0.0084	0.2141	-0.0508	0.2725	16.9396	-13.3164	9.7105

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 35 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 45 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 46 through 57 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 58 through 63 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 64 through 76 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 77 through 86 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 87 through 95 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 96 through 115 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 116 through 132 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 4 through 19 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 20 through 85 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 86 through 97 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 98 through 115 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 116 through 136 )

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