PDB-2r6c: Crystal Form BH2

ID or keywords:

Entry

Database: PDB / ID: 2r6c

Title

Crystal Form BH2

Components

DnaG Primase, Helicase Binding Domain
Replicative helicase

Keywords

REPLICATION / Helicase / Primase / dnaB / dnaG

Function / homology

Function and homology information

DNA primase DnaG / primosome complex / DNA primase activity / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding ...
Similarity search - Function

Biological species

Bacillus stearothermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 4 Å

Authors

Bailey, S. / Eliason, W.K. / Steitz, T.A.

Citation

Journal: Science / Year: 2007
Title: Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase
Authors: Bailey, S. / Eliason, W.K. / Steitz, T.A.

History

Deposition	Sep 5, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 10, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2r6c.cif.gz	477.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2r6c.ent.gz	404.5 KB	Display	PDB format
PDBx/mmJSON format	2r6c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2r6c_validation.pdf.gz	512 KB	Display	wwPDB validaton report
Full document	2r6c_full_validation.pdf.gz	630.3 KB	Display
Data in XML	2r6c_validation.xml.gz	96.6 KB	Display
Data in CIF	2r6c_validation.cif.gz	128.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r6/2r6c ftp://data.pdbj.org/pub/pdb/validation_reports/r6/2r6c	HTTPS FTP

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Related structure data

Related structure data	2r6aC 2r6dC 2r6eC C: citing same article (ref.)
Similar structure data	1svt-d 4v4o-2 4v4o-1 11908 1aon-d 1845 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	#168 - Dec 2013 DNA Helicase similarity (26) #73 - Jan 2006 Topoisomerase similarity (2)

Deposited unit

A: Replicative helicase

B: Replicative helicase

C: Replicative helicase

D: Replicative helicase

E: Replicative helicase

F: Replicative helicase

G: DnaG Primase, Helicase Binding Domain

H: DnaG Primase, Helicase Binding Domain

I: DnaG Primase, Helicase Binding Domain

355 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Replicative helicase

B: Replicative helicase

C: Replicative helicase

D: Replicative helicase

E: Replicative helicase

F: Replicative helicase

G: DnaG Primase, Helicase Binding Domain

H: DnaG Primase, Helicase Binding Domain

I: DnaG Primase, Helicase Binding Domain

A: Replicative helicase

B: Replicative helicase

C: Replicative helicase

D: Replicative helicase

E: Replicative helicase

F: Replicative helicase

G: DnaG Primase, Helicase Binding Domain

H: DnaG Primase, Helicase Binding Domain

I: DnaG Primase, Helicase Binding Domain

defined by author&software
709 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	228.775, 228.775, 192.984
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 domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
1	2	A
2	2	B
3	2	C
4	2	D
5	2	E
6	2	F
1	3	G
2	3	H
3	3	I

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	A	A	15 - 149	15 - 149
2	1	GLU	GLU	B	B	15 - 149	15 - 149
3	1	GLU	GLU	C	C	15 - 149	15 - 149
4	1	GLU	GLU	D	D	15 - 149	15 - 149
5	1	GLU	GLU	E	E	15 - 149	15 - 149
6	1	GLU	GLU	F	F	15 - 149	15 - 149
1	2	ILE	LEU	A	A	186 - 441	186 - 441
2	2	ILE	LEU	B	B	186 - 441	186 - 441
3	2	ILE	LEU	C	C	186 - 441	186 - 441
4	2	ILE	LEU	D	D	186 - 441	186 - 441
5	2	ILE	LEU	E	E	186 - 441	186 - 441
6	2	ILE	LEU	F	F	186 - 441	186 - 441
1	3	LEU	MSE	G	G	456 - 593	2 - 139
2	3	LEU	MSE	H	H	456 - 593	2 - 139
3	3	LEU	MSE	I	I	456 - 593	2 - 139

NCS ensembles :

ID
1
2
3

#1: Protein	Replicative helicase / DnaB Helicase Mass: 50699.445 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: DnaB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X4C9
#2: Protein	DnaG Primase, Helicase Binding Domain / E.C.2.7.7.- Mass: 16796.490 Da / Num. of mol.: 3 / Fragment: Helicase Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: DnaG / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9X4D0, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

#1: Protein

Replicative helicase / DnaB Helicase

Mass: 50699.445 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus stearothermophilus (bacteria) / Gene: DnaB / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X4C9

#2: Protein

DnaG Primase, Helicase Binding Domain / E.C.2.7.7.-

Mass: 16796.490 Da / Num. of mol.: 3 / Fragment: Helicase Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus stearothermophilus (bacteria) / Gene: DnaG / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9X4D0, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.11 Å³/Da / Density % sol: 70.08 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 0.5M Sodium Succinate, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2007
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 4→20 Å / Num. obs: 95194 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / R_sym value: 0.103 / Net I/σ(I): 19.5
Reflection shell	Resolution: 4→4.14 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 9534 / R_sym value: 0.503 / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SOLVE		phasing
REFMAC	5.2	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 4→20 Å / Cor.coef. F_o:F_c: 0.851 / Cor.coef. F_o:F_c free: 0.826 / SU B: 142.22 / SU ML: 0.91 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.99
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.34375	2218	5 %	RANDOM
R_work	0.32023	-	-	-
obs	0.32139	42380	90.76 %	-

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: 166.075 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.99 Å²	-2.5 Å²	0 Å²
2-	-	-4.99 Å²	0 Å²
3-	-	-	7.49 Å²

Refinement step

Cycle: LAST / Resolution: 4→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19920	0	0	0	19920

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	20154
X-RAY DIFFRACTION	r_angle_refined_deg	1.659	1.982	27216
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.833	5	2529
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.906	24.29	909
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.827	15	3705
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.096	15	174
X-RAY DIFFRACTION	r_chiral_restr	0.224	0.2	3219
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	14856
X-RAY DIFFRACTION	r_nbd_refined	0.273	0.2	9678
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	13704
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.26	0.2	708
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.326	0.2	68
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.18	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	0.912	3	13155
X-RAY DIFFRACTION	r_mcangle_it	1.256	4	20484
X-RAY DIFFRACTION	r_scbond_it	1.641	6	7781
X-RAY DIFFRACTION	r_scangle_it	2.117	9	6732

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1045	medium positional	0.14	0.5
1	2	B	1045	medium positional	0.15	0.5
1	3	C	1045	medium positional	0.16	0.5
1	4	D	1045	medium positional	0.16	0.5
1	5	E	1045	medium positional	0.16	0.5
1	6	F	1045	medium positional	0.15	0.5
2	1	A	1695	medium positional	0.13	0.5
2	2	B	1695	medium positional	0.11	0.5
2	3	C	1695	medium positional	0.14	0.5
2	4	D	1695	medium positional	0.14	0.5
2	5	E	1695	medium positional	0.13	0.5
2	6	F	1695	medium positional	0.19	0.5
3	1	G	1122	medium positional	0.11	0.5
3	2	H	1122	medium positional	0.11	0.5
3	3	I	1122	medium positional	0.11	0.5
1	1	A	1045	medium thermal	0.41	2
1	2	B	1045	medium thermal	0.4	2
1	3	C	1045	medium thermal	0.41	2
1	4	D	1045	medium thermal	0.43	2
1	5	E	1045	medium thermal	0.39	2
1	6	F	1045	medium thermal	0.38	2
2	1	A	1695	medium thermal	0.28	2
2	2	B	1695	medium thermal	0.24	2
2	3	C	1695	medium thermal	0.34	2
2	4	D	1695	medium thermal	0.25	2
2	5	E	1695	medium thermal	0.27	2
2	6	F	1695	medium thermal	0.3	2
3	1	G	1122	medium thermal	0.3	2
3	2	H	1122	medium thermal	0.33	2
3	3	I	1122	medium thermal	0.34	2

LS refinement shell

Resolution: 4→4.1 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.384	123	-
R_work	0.34	2504	-
obs	-	-	74.86 %

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	16.216	-9.8503	-0.4882	10.8069	1.0553	5.7913	-0.0443	-0.1731	0.3261	-0.1458	0.132	0.0845	0.2509	-0.1537	-0.0877	-0.8968	0.0607	0.0013	-1.3569	-0.1021	-0.9874	79.7394	-50.6402	5.6586
2	9.7086	3.4785	1.4468	9.2872	-1.8987	8.2092	-0.2073	-1.4301	0.0017	0.0795	-0.0943	0.0753	0.033	0.176	0.3015	-0.673	0.1725	0.0741	-0.3079	0.1274	-0.8075	106.2524	-29.2305	41.5065
3	4.091	4.0785	1.4708	22.8762	0.0017	0.6428	0.1729	-0.1985	0.8325	0.1712	-0.0596	0.3572	-0.3636	0.127	-0.1132	-0.7603	0.0952	0.3389	-1.0054	-0.0619	-0.7315	100.6263	-20.0526	7.6522
4	8.2425	1.2376	1.8537	8.8896	-1.5162	10.7206	0.1329	-0.0266	-0.0043	-0.2288	-0.1933	0.5474	0.4159	0.3854	0.0604	-0.5246	0.2294	0.0895	0.3351	0.1301	-0.4335	110.0712	11.7127	41.9891
5	21.6249	6.9444	3.4376	5.2245	0.765	6.8762	0.2149	0.2756	0.4602	0.0087	-0.0493	-0.3838	-0.265	0.2467	-0.1656	-1.2033	0.0764	-0.0106	-1.1184	0.055	-0.9113	30.7676	13.6588	5.3514
6	6.5638	-0.4908	-1.7036	12.7528	0.3861	10.2151	0.1323	-0.8053	0.0617	1.0547	-0.0911	-0.4079	0.0668	0.1975	-0.0412	-0.7599	-0.0171	-0.0369	-0.558	-0.0632	-1.1202	36.063	-12.0391	40.4308
7	15.2482	-8.7365	0.204	10.798	-1.6036	1.1523	0.2113	-0.5469	0.42	0.0584	0.0194	-0.8779	0.231	0.3227	-0.2307	-1.0989	0.0336	-0.1434	-0.8445	-0.1196	-1.0345	46.9719	-19.6397	7.012
8	8.5136	0.3798	-2.0362	7.4695	-0.1415	11.0557	0.1928	-0.1284	0.2427	-0.1001	-0.0955	-0.2952	0.2266	-0.8805	-0.0973	-0.0774	-0.3903	0.0842	-0.2045	0.0679	-1.0238	68.8966	-41.0404	42.1331
9	3.3654	2.0945	-1.0263	21.3932	-1.5497	6.4222	-0.1325	0.2528	-0.5222	0.2614	0.2278	0.0479	0.2049	0.274	-0.0953	-1.2176	-0.101	0.15	-0.9427	0.001	-0.6758	111.0705	23.8293	5.0748
10	10.5732	-1.8027	0.2927	7.0059	0.9751	9.5616	-0.2932	-0.6625	-0.3545	0.8749	0.1576	-0.0239	-0.0128	0.1541	0.1357	-0.5755	0.0022	0.027	-0.5966	0.0785	-0.8389	81.9735	39.1797	39.9456
11	20.4457	5.9057	-0.4882	4.0876	0.5049	1.3469	0.0682	-0.1534	-0.6406	0.2505	0.0299	0.1757	0.2811	-0.2424	-0.0981	-1.0198	-0.1675	0.0741	-0.8892	0.0802	-0.6303	74.0504	26.2572	6.9168
12	9.5227	2.6358	-0.9703	8.0039	1.0983	7.865	0.0262	0.0778	-0.2602	0.1994	-0.2107	-0.8459	-1.1763	2.3382	0.1845	0.1383	-0.2735	0.12	0.7833	0.0347	-0.6549	45.0211	25.3281	43.4715
13	19.1219	-3.422	-0.8662	16.4539	0.3471	12.9552	0.2265	1.0526	1.1912	-0.7738	0.34	-2.0797	-1.4978	1.8747	-0.5665	-0.6947	0.0147	0.4673	-0.0294	-0.0427	-0.4715	126.7259	-35.3277	-2.0472
14	23.5878	6.9731	-4.217	26.2056	10.5251	6.4934	-0.2056	1.5461	-0.8119	0.8457	1.4494	-1.3346	-0.2243	2.3847	-1.2438	-0.0967	-0.0014	0.0898	-0.6218	-0.0583	-0.4933	103.7381	-59.6709	-4.9753
15	17.6731	5.116	3.7277	18.3316	7.2609	18.8099	0.3815	0.2367	-1.705	-0.3428	0.2676	-0.2619	2.1164	0.3888	-0.649	-0.5547	-0.0755	-0.1903	-0.8771	-0.0832	-0.9925	21.4748	-34.5506	-4.3782
16	18.5692	-4.8987	10.9407	30.1195	-1.5944	6.504	0.4037	-0.434	-0.9665	-2.037	1.0261	0.9614	2.3599	-0.54	-1.4298	-0.5772	0.1036	0.0769	-0.6532	-0.1742	-0.5333	11.2468	-2.6006	-6.242
17	16.0638	-0.7708	3.2678	19.6631	-2.2636	15.6289	0.6649	0.9502	1.8532	-0.4923	0.0938	1.3886	-0.8893	-2.2999	-0.7587	-0.7035	0.2478	0.1799	-0.3767	0.4445	-0.0319	73.9188	56.0274	-4.3368

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	15 - 149	15 - 149
2	X-RAY DIFFRACTION	2	A	A	186 - 441	186 - 441
3	X-RAY DIFFRACTION	3	B	B	15 - 149	15 - 149
4	X-RAY DIFFRACTION	4	B	B	186 - 441	186 - 441
5	X-RAY DIFFRACTION	5	C	C	15 - 149	15 - 149
6	X-RAY DIFFRACTION	6	C	C	186 - 441	186 - 441
7	X-RAY DIFFRACTION	7	D	D	15 - 149	15 - 149
8	X-RAY DIFFRACTION	8	D	D	186 - 441	186 - 441
9	X-RAY DIFFRACTION	9	E	E	15 - 149	15 - 149
10	X-RAY DIFFRACTION	10	E	E	186 - 441	186 - 441
11	X-RAY DIFFRACTION	11	F	F	15 - 149	15 - 149
12	X-RAY DIFFRACTION	12	F	F	186 - 441	186 - 441
13	X-RAY DIFFRACTION	13	G	G	461 - 555	7 - 101
14	X-RAY DIFFRACTION	14	G	G	556 - 593	102 - 139
15	X-RAY DIFFRACTION	15	H	H	461 - 555	7 - 101
16	X-RAY DIFFRACTION	16	H	H	556 - 593	102 - 139
17	X-RAY DIFFRACTION	17	I	I	461 - 555	7 - 101

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