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- PDB-2r6d: Crystal Form B1 -

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Basic information

Entry
Database: PDB / ID: 2r6d
TitleCrystal Form B1
ComponentsReplicative helicase
KeywordsREPLICATION / Helicase / Replication DnaB / Hexameric
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA helicase, DnaB type / 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. ...DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA helicase, DnaB type / 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. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Replicative DNA helicase
Similarity search - Component
Biological speciesBacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.7 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 / Refinement description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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


Theoretical massNumber of molelcules
Total (without water)304,1976
Polymers304,1976
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22550 Å2
ΔGint-131 kcal/mol
Surface area104170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)371.260, 110.295, 112.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F

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
11PROPROGLUGLUAA10 - 14910 - 149
21PROPROGLUGLUBB10 - 14910 - 149
31PROPROGLUGLUCC10 - 14910 - 149
41PROPROGLUGLUDD10 - 14910 - 149
51PROPROGLUGLUEE10 - 14910 - 149
61PROPROGLUGLUFF10 - 14910 - 149
12ILEILELEULEUAA186 - 441186 - 441
22ILEILELEULEUBB186 - 441186 - 441
32ILEILELEULEUCC186 - 441186 - 441
42ILEILELEULEUDD186 - 441186 - 441
52ILEILELEULEUEE186 - 441186 - 441
62ILEILELEULEUFF186 - 441186 - 441

NCS ensembles :
ID
1
2

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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

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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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 1.0M Ammonium Acetate, pH 5.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 92787 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rsym value: 0.081 / Net I/σ(I): 15
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 8286 / Rsym value: 0.59 / % possible all: 86.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 3.7→20 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.886 / SU B: 126.82 / SU ML: 0.848 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.762
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.32228 2501 5.1 %RANDOM
Rwork0.30897 ---
all0.30966 46513 --
obs0.30966 46513 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 177.291 Å2
Baniso -1Baniso -2Baniso -3
1-13.74 Å20 Å20 Å2
2---13.58 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 3.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18085 0 0 0 18085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02218282
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9824693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59552308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59424.553817
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.33153350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8215153
X-RAY DIFFRACTIONr_chiral_restr0.1850.22941
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213444
X-RAY DIFFRACTIONr_nbd_refined0.2510.28505
X-RAY DIFFRACTIONr_nbtor_refined0.3110.212387
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2616
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5050.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.23
X-RAY DIFFRACTIONr_mcbond_it0.799311991
X-RAY DIFFRACTIONr_mcangle_it1.256418746
X-RAY DIFFRACTIONr_scbond_it1.51266943
X-RAY DIFFRACTIONr_scangle_it2.38295947
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1077medium positional0.680.5
12B1077medium positional0.360.5
13C1077medium positional0.420.5
14D1077medium positional0.410.5
15E1077medium positional0.360.5
16F1077medium positional0.420.5
21A1796medium positional0.170.5
22B1796medium positional0.150.5
23C1796medium positional0.130.5
24D1796medium positional0.140.5
25E1796medium positional0.110.5
26F1796medium positional0.130.5
11A1077medium thermal0.452
12B1077medium thermal0.52
13C1077medium thermal0.52
14D1077medium thermal0.42
15E1077medium thermal0.372
16F1077medium thermal0.432
21A1796medium thermal0.482
22B1796medium thermal0.442
23C1796medium thermal0.32
24D1796medium thermal0.292
25E1796medium thermal0.292
26F1796medium thermal0.292
LS refinement shellResolution: 3.7→3.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 158 -
Rwork0.36 2929 -
obs--87.01 %
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)
12.57160.3517-3.41466.2636-2.488816.2508-0.06020.0893-0.7219-0.5281-0.2525-0.32711.1160.32760.3127-1.07530.27680.2079-0.55210.1252-0.790561.5959-20.3194-57.2402
23.5573-0.69491.332911.2948-3.52835.5908-0.1651-0.45790.11750.7402-0.13-1.19750.07930.64230.2951-1.1710.17750.4834-0.3235-0.0619-0.342780.026821.2539-46.6512
39.9189-10.1449-7.262515.3449.10548.01850.0818-0.18740.1206-0.5561-0.19680.5508-0.4975-0.13990.115-1.31650.13670.2085-0.50180.0717-0.749645.079311.9374-50.1583
48.1295-0.5604-0.84527.43684.317110.4833-0.168-0.23-0.58911.20140.1495-0.61660.11560.44270.0185-0.94170.1230.1771-0.68890.1718-0.602964.078243.9955-21.8413
59.3467-7.5344-3.471115.02914.31085.5780.52680.07060.0046-0.3991-0.02390.1004-1.15870.0182-0.5029-1.52510.34740.136-0.2780.0734-0.468917.824541.7564-30.6586
69.46453.4361-1.893810.7752-1.573114.2185-0.1708-0.28130.0331-0.10590.70870.57881.0062-0.0334-0.5379-0.13740.12290.0398-0.67950.2248-0.508541.362937.28926.0831
70.627-1.95572.091721.2048-11.23388.44640.01840.0378-0.12590.35150.29970.490.3675-0.4818-0.3181-1.20190.36130.3164-0.40730.0425-0.114515.303314.701-5.3478
87.264-1.50511.942510.0841-1.119910.158-0.21440.4116-0.01420.1451-0.0345-0.1956-0.6480.73560.24890.05820.10560.2111-0.60150.2288-0.890848.59423.053621.6315
93.4516-1.65161.743718.8669-4.89867.1292-0.231-0.5673-0.31291.1190.45511.11610.4152-0.5352-0.224-0.65730.16780.7427-0.40250.2997-0.371522.1409-25.645813.2327
1014.3848-1.4611.44477.0275-1.60728.7704-0.4457-0.45440.96710.13740.009-0.7082-0.08230.42220.43670.74210.2954-0.17640.28320.0434-0.1378.1362-19.5925-0.1571
113.62080.2702-6.11984.9713-3.474518.2678-0.02080.04870.13710.1002-0.13530.165-0.72120.05760.1561-0.84950.14180.2165-0.75020.1958-0.900144.9036-28.3208-16.1641
124.05180.7416-0.15029.0915-1.190711.5427-0.0113-1.75240.22221.15940.0287-0.7633-0.108-0.1285-0.0174-0.70080.23720.22410.03240.0036-0.192690.4801-8.0921-35.7702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 149
2X-RAY DIFFRACTION2A180 - 441
3X-RAY DIFFRACTION2F160 - 174
4X-RAY DIFFRACTION3B10 - 149
5X-RAY DIFFRACTION4B183 - 441
6X-RAY DIFFRACTION4C160 - 174
7X-RAY DIFFRACTION5C10 - 149
8X-RAY DIFFRACTION6C183 - 441
9X-RAY DIFFRACTION7D10 - 149
10X-RAY DIFFRACTION8D183 - 441
11X-RAY DIFFRACTION8E160 - 174
12X-RAY DIFFRACTION9E10 - 149
13X-RAY DIFFRACTION10E183 - 441
14X-RAY DIFFRACTION11F10 - 149
15X-RAY DIFFRACTION12F183 - 441
16X-RAY DIFFRACTION12A160 - 174

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