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- PDB-2r6c: Crystal Form BH2 -

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Basic information

Entry
Database: PDB / ID: 2r6c
TitleCrystal Form BH2
Components
  • DnaG Primase, Helicase Binding Domain
  • Replicative helicase
KeywordsREPLICATION / Helicase / Primase / dnaB / dnaG
Function / homology
Function and homology information


DNA primase DnaG / primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer / DNA-directed RNA polymerase complex / DNA helicase activity / DNA-directed RNA polymerase activity / ATP hydrolysis activity / DNA binding / zinc ion binding ...DNA primase DnaG / primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer / DNA-directed RNA polymerase complex / DNA helicase activity / DNA-directed RNA polymerase activity / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #360 / DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain ...Helix Hairpins - #360 / DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA primase, catalytic core, N-terminal domain superfamily / : / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / DNA Primase, CHC2-type zinc finger / DNA helicase, DnaB type / Toprim-like / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / TOPRIM / DEAD-box subfamily ATP-dependent helicases signature. / Toprim domain profile. / TOPRIM domain / Helix Hairpins / Helix non-globular / Special / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Replicative DNA helicase DnaB / DNA primase
Similarity search - Component
Biological speciesBacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4 Å
AuthorsBailey, S. / Eliason, W.K. / Steitz, T.A.
CitationJournal: 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
DepositionSep 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)354,5869
Polymers354,5869
Non-polymers00
Water00
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


Theoretical massNumber of molelcules
Total (without water)709,17218
Polymers709,17218
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area42590 Å2
ΔGint-258 kcal/mol
Surface area241290 Å2
MethodPISA
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 number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F
13G
23H
33I

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLUAA15 - 14915 - 149
21GLUGLUGLUGLUBB15 - 14915 - 149
31GLUGLUGLUGLUCC15 - 14915 - 149
41GLUGLUGLUGLUDD15 - 14915 - 149
51GLUGLUGLUGLUEE15 - 14915 - 149
61GLUGLUGLUGLUFF15 - 14915 - 149
12ILEILELEULEUAA186 - 441186 - 441
22ILEILELEULEUBB186 - 441186 - 441
32ILEILELEULEUCC186 - 441186 - 441
42ILEILELEULEUDD186 - 441186 - 441
52ILEILELEULEUEE186 - 441186 - 441
62ILEILELEULEUFF186 - 441186 - 441
13LEULEUMSEMSEGG456 - 5932 - 139
23LEULEUMSEMSEHH456 - 5932 - 139
33LEULEUMSEMSEII456 - 5932 - 139

NCS ensembles :
ID
1
2
3

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Components

#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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.08 %
Crystal growTemperature: 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

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

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 4→20 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.34375 2218 5 %RANDOM
Rwork0.32023 ---
obs0.32139 42380 90.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 166.075 Å2
Baniso -1Baniso -2Baniso -3
1--4.99 Å2-2.5 Å20 Å2
2---4.99 Å20 Å2
3---7.49 Å2
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19920 0 0 0 19920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02220154
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.98227216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.83352529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90624.29909
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.827153705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.09615174
X-RAY DIFFRACTIONr_chiral_restr0.2240.23219
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214856
X-RAY DIFFRACTIONr_nbd_refined0.2730.29678
X-RAY DIFFRACTIONr_nbtor_refined0.3150.213704
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.260.2708
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3260.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.24
X-RAY DIFFRACTIONr_mcbond_it0.912313155
X-RAY DIFFRACTIONr_mcangle_it1.256420484
X-RAY DIFFRACTIONr_scbond_it1.64167781
X-RAY DIFFRACTIONr_scangle_it2.11796732
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1045medium positional0.140.5
12B1045medium positional0.150.5
13C1045medium positional0.160.5
14D1045medium positional0.160.5
15E1045medium positional0.160.5
16F1045medium positional0.150.5
21A1695medium positional0.130.5
22B1695medium positional0.110.5
23C1695medium positional0.140.5
24D1695medium positional0.140.5
25E1695medium positional0.130.5
26F1695medium positional0.190.5
31G1122medium positional0.110.5
32H1122medium positional0.110.5
33I1122medium positional0.110.5
11A1045medium thermal0.412
12B1045medium thermal0.42
13C1045medium thermal0.412
14D1045medium thermal0.432
15E1045medium thermal0.392
16F1045medium thermal0.382
21A1695medium thermal0.282
22B1695medium thermal0.242
23C1695medium thermal0.342
24D1695medium thermal0.252
25E1695medium thermal0.272
26F1695medium thermal0.32
31G1122medium thermal0.32
32H1122medium thermal0.332
33I1122medium thermal0.342
LS refinement shellResolution: 4→4.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 123 -
Rwork0.34 2504 -
obs--74.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
116.216-9.8503-0.488210.80691.05535.7913-0.0443-0.17310.3261-0.14580.1320.08450.2509-0.1537-0.0877-0.89680.06070.0013-1.3569-0.1021-0.987479.7394-50.64025.6586
29.70863.47851.44689.2872-1.89878.2092-0.2073-1.43010.00170.0795-0.09430.07530.0330.1760.3015-0.6730.17250.0741-0.30790.1274-0.8075106.2524-29.230541.5065
34.0914.07851.470822.87620.00170.64280.1729-0.19850.83250.1712-0.05960.3572-0.36360.127-0.1132-0.76030.09520.3389-1.0054-0.0619-0.7315100.6263-20.05267.6522
48.24251.23761.85378.8896-1.516210.72060.1329-0.0266-0.0043-0.2288-0.19330.54740.41590.38540.0604-0.52460.22940.08950.33510.1301-0.4335110.071211.712741.9891
521.62496.94443.43765.22450.7656.87620.21490.27560.46020.0087-0.0493-0.3838-0.2650.2467-0.1656-1.20330.0764-0.0106-1.11840.055-0.911330.767613.65885.3514
66.5638-0.4908-1.703612.75280.386110.21510.1323-0.80530.06171.0547-0.0911-0.40790.06680.1975-0.0412-0.7599-0.0171-0.0369-0.558-0.0632-1.120236.063-12.039140.4308
715.2482-8.73650.20410.798-1.60361.15230.2113-0.54690.420.05840.0194-0.87790.2310.3227-0.2307-1.09890.0336-0.1434-0.8445-0.1196-1.034546.9719-19.63977.012
88.51360.3798-2.03627.4695-0.141511.05570.1928-0.12840.2427-0.1001-0.0955-0.29520.2266-0.8805-0.0973-0.0774-0.39030.0842-0.20450.0679-1.023868.8966-41.040442.1331
93.36542.0945-1.026321.3932-1.54976.4222-0.13250.2528-0.52220.26140.22780.04790.20490.274-0.0953-1.2176-0.1010.15-0.94270.001-0.6758111.070523.82935.0748
1010.5732-1.80270.29277.00590.97519.5616-0.2932-0.6625-0.35450.87490.1576-0.0239-0.01280.15410.1357-0.57550.00220.027-0.59660.0785-0.838981.973539.179739.9456
1120.44575.9057-0.48824.08760.50491.34690.0682-0.1534-0.64060.25050.02990.17570.2811-0.2424-0.0981-1.0198-0.16750.0741-0.88920.0802-0.630374.050426.25726.9168
129.52272.6358-0.97038.00391.09837.8650.02620.0778-0.26020.1994-0.2107-0.8459-1.17632.33820.18450.1383-0.27350.120.78330.0347-0.654945.021125.328143.4715
1319.1219-3.422-0.866216.45390.347112.95520.22651.05261.1912-0.77380.34-2.0797-1.49781.8747-0.5665-0.69470.01470.4673-0.0294-0.0427-0.4715126.7259-35.3277-2.0472
1423.58786.9731-4.21726.205610.52516.4934-0.20561.5461-0.81190.84571.4494-1.3346-0.22432.3847-1.2438-0.0967-0.00140.0898-0.6218-0.0583-0.4933103.7381-59.6709-4.9753
1517.67315.1163.727718.33167.260918.80990.38150.2367-1.705-0.34280.2676-0.26192.11640.3888-0.649-0.5547-0.0755-0.1903-0.8771-0.0832-0.992521.4748-34.5506-4.3782
1618.5692-4.898710.940730.1195-1.59446.5040.4037-0.434-0.9665-2.0371.02610.96142.3599-0.54-1.4298-0.57720.10360.0769-0.6532-0.1742-0.533311.2468-2.6006-6.242
1716.0638-0.77083.267819.6631-2.263615.62890.66490.95021.8532-0.49230.09381.3886-0.8893-2.2999-0.7587-0.70350.24780.1799-0.37670.4445-0.031973.918856.0274-4.3368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 14915 - 149
2X-RAY DIFFRACTION2AA186 - 441186 - 441
3X-RAY DIFFRACTION3BB15 - 14915 - 149
4X-RAY DIFFRACTION4BB186 - 441186 - 441
5X-RAY DIFFRACTION5CC15 - 14915 - 149
6X-RAY DIFFRACTION6CC186 - 441186 - 441
7X-RAY DIFFRACTION7DD15 - 14915 - 149
8X-RAY DIFFRACTION8DD186 - 441186 - 441
9X-RAY DIFFRACTION9EE15 - 14915 - 149
10X-RAY DIFFRACTION10EE186 - 441186 - 441
11X-RAY DIFFRACTION11FF15 - 14915 - 149
12X-RAY DIFFRACTION12FF186 - 441186 - 441
13X-RAY DIFFRACTION13GG461 - 5557 - 101
14X-RAY DIFFRACTION14GG556 - 593102 - 139
15X-RAY DIFFRACTION15HH461 - 5557 - 101
16X-RAY DIFFRACTION16HH556 - 593102 - 139
17X-RAY DIFFRACTION17II461 - 5557 - 101

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