PDB-2v79: Crystal Structure of the N-terminal domain of DnaD from Bacillus ...

ID or keywords:

Entry

Database: PDB / ID: 2v79

Title

Crystal Structure of the N-terminal domain of DnaD from Bacillus Subtilis

Components

DNA REPLICATION PROTEIN DNAD

Keywords

DNA BINDING PROTEIN / PRIMOSOME / DNA-BINDING PROTEIN

Function / homology

Function and homology information

primosome complex / DNA replication, synthesis of primer
Similarity search - Function

Biological species

BACILLUS SUBTILIS (bacteria)

Method

X-RAY DIFFRACTION /

MAD / Resolution: 2 Å

Authors

Schneider, S. / Zhang, W. / Soultanas, P. / Paoli, M.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Structure of the N-Terminal Oligomerization Domain of Dnad Reveals a Unique Tetramerization Motif and Provides Insights Into Scaffold Formation.
Authors: Schneider, S. / Zhang, W. / Soultanas, P. / Paoli, M.

History

Deposition	Jul 27, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 15, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Refinement description / Version format compliance
Revision 1.2	Jun 28, 2017	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3	May 8, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2v79.cif.gz	69.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2v79.ent.gz	53.6 KB	Display	PDB format
PDBx/mmJSON format	2v79.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v7/2v79 ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v79	HTTPS FTP

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Related structure data

Similar structure data	1ocx-d 1ue5-1 3hjj-d 1qrm-1 5u2k-1 1h7z-d 3drz-d 3ol9-3 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

Deposited unit

A: DNA REPLICATION PROTEIN DNAD

B: DNA REPLICATION PROTEIN DNAD

hetero molecules

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

1

A: DNA REPLICATION PROTEIN DNAD

B: DNA REPLICATION PROTEIN DNAD

hetero molecules

A: DNA REPLICATION PROTEIN DNAD

B: DNA REPLICATION PROTEIN DNAD

hetero molecules

defined by author&software
65.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.666, 78.666, 124.558
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (-0.8548, -0.09045, -0.511), (-0.06449, -0.9586, 0.2775), (-0.515, 0.2702, 0.8135)
Vector: 38.05, 66.13, 0.6889)

#1: Protein	DNA REPLICATION PROTEIN DNAD Mass: 16079.396 Da / Num. of mol.: 2 / Fragment: N-TERMINAL OLIGOMERIZATION DOMAIN, RESIDUES 1-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 EMG50 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3), B834 (DE3) / References: UniProt: P39787
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE N-TERMINAL DOMAIN INCLUDES RESIDUES 1-128 WITH AN ADDITIONAL LE LINKER BEFORE THE HIS6-TAG

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.3 Å³/Da / Density % sol: 62.9 % / Description: NONE
Crystal grow	Details: 0.1M SODIUMACETATE, 3.2M SODIUMCHLORIDE

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
Detector	Type: RIGAKU IMAGE-PLATE / Detector: IMAGE PLATE / Date: May 27, 2006 / Details: VARIMAX HF OPTICS
Radiation	Monochromator: NI FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2→28 Å / Num. obs: 30662 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / R_merge(I) obs: 0.05 / Net I/σ(I): 24.4
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.38 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
SHARP		phasing

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 2→30 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.949 / SU B: 4.638 / SU ML: 0.074 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21	1542	5 %	RANDOM
R_work	0.181	-	-	-
obs	0.182	29103	99.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 25.71 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.9 Å²	0.45 Å²	0 Å²
2-	-	0.9 Å²	0 Å²
3-	-	-	-1.35 Å²

Refinement step

Cycle: LAST / Resolution: 2→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1919	0	14	231	2164

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1944
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.126	1.982	2615
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.049	5	233
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.448	26	95
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.226	15	397
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.937	15	5
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	286
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1429
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	885
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	1349
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	188
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	0.157	0.2	67
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.203	0.2	18
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	0.512	1.5	1143
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.939	2	1852
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.53	3	821
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.541	4.5	759
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: 2→2.05 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.306	112
R_work	0.253	2119

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	21.8794	-8.0396	-1.2764	7.59	0.5312	9.9805	0.1594	-0.5914	1.0091	0.1803	0.0732	0.0362	-1.1972	0.0486	-0.2326	0.1771	-0.0154	0.0266	-0.0291	-0.0606	0.1295	14.3254	-13.655	-44.5361
2	2.5588	-6.2496	2.7206	32.3306	-14.6749	7.5958	0.024	0.0364	0.0923	0.4941	-0.0349	0.0235	-0.3287	0.2083	0.0109	0.0817	-0.0322	-0.0162	0.1235	-0.0102	0.0717	21.4042	-27.3268	-40.4942
3	9.4306	-2.6996	6.7179	1.5788	1.3452	18.038	0.5918	-0.3762	-0.9075	0.2004	-0.2454	0.059	1.6805	-0.2923	-0.3464	0.1216	-0.0945	-0.081	0.0892	0.1005	0.115	24.0633	-41.3426	-27.9601
4	1.7857	-0.4746	0.8993	3.2538	-2.6173	7.4332	0.0301	-0.1812	0.1248	0.0362	-0.0516	-0.0921	0.0357	0.0724	0.0215	-0.0103	-0.0365	-0.042	0.1627	-0.0222	0.0618	29.5988	-30.5783	-30.1131
5	15.5809	8.168	11.438	10.0637	0.604	18.8101	-0.2768	0.7918	0.7857	-0.3596	0.1008	0.5614	-0.3775	0.6838	0.176	0.0499	-0.0764	-0.0058	0.1512	0.0519	0.0329	33.0959	-24.6856	-42.4888
6	19.3343	3.3947	-10.8942	2.8625	3.2589	17.9395	0.1273	0.384	0.7876	-0.007	-0.1363	-0.0206	-0.7264	0.2429	0.009	0.095	-0.0741	-0.0876	0.1183	0.0531	0.1333	35.3742	-19.8461	-31.3277
7	3.7246	-4.1127	0.1508	8.0087	-0.3108	3.2529	-0.0568	-0.0694	0.219	0.2679	-0.1193	0.0109	-0.1779	0.2604	0.176	-0.0488	-0.0503	-0.0466	0.2001	-0.0046	0.0012	37.0703	-28.2065	-24.7498
8	27.9496	-6.1303	-28.4559	33.7688	-19.2459	94.5016	-0.5432	1.0124	-0.7444	-0.9819	0.0536	-1.1801	2.479	1.4135	0.4895	-0.0218	0.0422	-0.0399	0.2938	-0.0029	0.058	44.0245	-32.5544	-37.6722
9	4.7198	7.3727	0.1192	21.1958	-4.2576	5.4942	-0.0786	-0.1263	-0.1839	-0.5955	-0.2309	-0.8139	0.2754	0.9092	0.3095	-0.0173	0.0782	0.0093	0.2802	0.0067	0.0243	37.4769	-36.8817	-36.4454
10	49.3855	11.7366	3.188	83.3599	-21.291	15.5826	0.4645	-2.2641	-2.4815	0.721	0.5324	1.741	1.9015	-0.7124	-0.9969	0.3772	-0.0216	-0.1128	0.1384	0.2344	0.2549	28.5268	-53.3335	-30.0196
11	24.142	-0.9906	0.5301	15.9415	0.4929	13.2599	-0.3763	-0.3699	-1.4649	0.5823	0.212	-0.6236	1.133	0.5033	0.1642	0.1916	0.1111	-0.0153	-0.0037	0.0362	0.1086	23.4437	-53.4804	-41.1632
12	0.1167	-1.8326	-0.682	32.4638	7.9786	6.0218	-0.1147	-0.0842	-0.0005	0.1112	0.0656	-0.1204	0.2613	0.1133	0.0492	0.0694	-0.0322	0.0262	0.1205	-0.0163	0.0857	18.7146	-40.4641	-38.1279
13	3.7906	-0.199	-1.42	3.4571	2.195	6.5061	0.1858	-0.251	0.3141	-0.0634	-0.2135	-0.1071	-0.8023	0.2261	0.0277	0.0398	-0.0596	0.0024	0.078	-0.0537	0.105	20.2849	-22.0745	-28.3553
14	5.2635	3.3856	2.533	4.4071	1.8237	5.9424	-0.0865	-0.0083	-0.2215	-0.0664	-0.046	0.0826	-0.0284	-0.0201	0.1325	-0.0241	-0.0014	0.047	0.1749	-0.0395	0.0664	13.633	-35.0928	-28.924
15	14.8591	0.6569	4.1914	1.2867	-1.5411	3.7291	-0.0448	-0.1758	-0.7065	0.0827	0.0111	0.111	0.2112	0.0045	0.0337	-0.0094	0.0253	0.0562	0.1427	-0.0041	0.0723	12.9052	-40.3914	-21.8011
16	16.5252	-11.784	-4.707	15.7233	2.1467	5.0481	-0.5072	-1.1487	-0.2019	1.1254	0.1439	0.1027	0.2557	0.4218	0.3633	0.0403	0.0051	0.0423	0.2342	0.0044	-0.0501	15.2174	-35.4252	-13.4431
17	10.5464	-8.7072	6.7053	23.6278	-8.01	14.2568	-0.1219	-0.6334	0.5808	0.5767	0.0771	-0.124	-0.6747	0.0533	0.0448	0.0061	-0.0159	0.055	0.1916	-0.095	0.0041	9.3869	-27.0994	-17.3295
18	18.6619	8.8997	4.5769	6.4225	3.1827	3.7221	0.0722	0.2602	0.4275	-0.0735	0.1379	0.1454	-0.3113	-0.3588	-0.2101	-0.0231	0.021	0.0154	0.1533	-0.0128	0.025	2.1111	-29.6335	-25.6027
19	23.2272	7.4967	0.9545	14.9363	-12.2676	18.1499	0.0798	1.2309	-1.3838	-1.8351	0.1656	1.0599	1.7296	-1.3585	-0.2454	0.2103	-0.0736	-0.0919	0.3514	-0.1168	0.2209	-7.7232	-41.2637	-31.0172
20	5.4117	9.4844	-4.4726	17.6137	-7.0141	4.3819	-0.1849	0.0806	0.2929	-0.3615	0.2476	0.3056	0.0159	-0.4203	-0.0627	0.0017	0.0316	0.0101	0.1649	-0.0325	0.065	5.8226	-28.8124	-29.0286
21	11.7443	8.1605	-0.4395	28.5311	-0.6264	9.399	-0.2812	-0.0674	1.5073	-0.6916	0.1597	-0.4739	-1.4438	0.0105	0.1215	0.2795	0.0111	0.016	-0.0296	-0.0367	0.2845	13.2577	-11.4458	-33.2903

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 9
2	X-RAY DIFFRACTION	2	A	10 - 18
3	X-RAY DIFFRACTION	3	A	19 - 27
4	X-RAY DIFFRACTION	4	A	28 - 45
5	X-RAY DIFFRACTION	5	A	46 - 50
6	X-RAY DIFFRACTION	6	A	51 - 59
7	X-RAY DIFFRACTION	7	A	60 - 81
8	X-RAY DIFFRACTION	8	A	82 - 87
9	X-RAY DIFFRACTION	9	A	92 - 108
10	X-RAY DIFFRACTION	10	A	109 - 115
11	X-RAY DIFFRACTION	11	B	1 - 8
12	X-RAY DIFFRACTION	12	B	9 - 17
13	X-RAY DIFFRACTION	13	B	18 - 33
14	X-RAY DIFFRACTION	14	B	34 - 49
15	X-RAY DIFFRACTION	15	B	50 - 62
16	X-RAY DIFFRACTION	16	B	63 - 70
17	X-RAY DIFFRACTION	17	B	71 - 78
18	X-RAY DIFFRACTION	18	B	79 - 86
19	X-RAY DIFFRACTION	19	B	87 - 94
20	X-RAY DIFFRACTION	20	B	95 - 104
21	X-RAY DIFFRACTION	21	B	105 - 117

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Yorodumi