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- PDB-2q6t: Crystal structure of the Thermus aquaticus DnaB monomer -

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Basic information

Entry
Database: PDB / ID: 2q6t
TitleCrystal structure of the Thermus aquaticus DnaB monomer
ComponentsDnaB replication fork helicase
KeywordsHYDROLASE / Replication / helicase / DnaB
Function / homology
Function and homology information


DNA 5'-3' helicase / primosome complex / DNA replication, synthesis of primer / DNA helicase activity / hydrolase activity / DNA binding / ATP 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 / 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
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsBailey, S. / Eliason, W.K. / Steitz, T.A.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: The crystal structure of the Thermus aquaticus DnaB helicase monomer.
Authors: Bailey, S. / Eliason, W.K. / Steitz, T.A.
History
DepositionJun 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DnaB replication fork helicase
B: DnaB replication fork helicase
C: DnaB replication fork helicase
D: DnaB replication fork helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5868
Polymers195,2024
Non-polymers3844
Water45025
1
A: DnaB replication fork helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8972
Polymers48,8011
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DnaB replication fork helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8972
Polymers48,8011
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DnaB replication fork helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8972
Polymers48,8011
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DnaB replication fork helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8972
Polymers48,8011
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.707, 104.707, 363.258
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
DnaB replication fork helicase


Mass: 48800.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: dnab / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9Z693, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 1.3M Ammonium Sulfate, 10mM Magnesium Sulfate, 5% 1,6-hexanediol, 100mM MES, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1404
SYNCHROTRONAPS 19-ID20.97935, 0.97949, 0.96411
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 5, 2001
ADSC QUANTUM 3152CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.14041
20.979351
30.979491
40.964111
ReflectionResolution: 2.9→30 Å / Num. all: 51424 / Num. obs: 47366 / % possible obs: 99.17 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 15.8
Reflection shellResolution: 2.9→2.974 Å / Mean I/σ(I) obs: 1.9 / % possible all: 99.92

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / SU B: 44.604 / SU ML: 0.376 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.429
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.28453 2638 5.1 %RANDOM
Rwork0.24085 ---
obs0.243 49121 99.17 %-
all-51424 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 104.751 Å2
Baniso -1Baniso -2Baniso -3
1-4.93 Å22.47 Å20 Å2
2--4.93 Å20 Å2
3----7.4 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12701 0 20 25 12746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02212895
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.98817428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.08151624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30723.591582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.655152305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.37915128
X-RAY DIFFRACTIONr_chiral_restr0.0820.22013
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029619
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.25911
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.28854
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2392
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7421.58448
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.224213061
X-RAY DIFFRACTIONr_scbond_it1.93234950
X-RAY DIFFRACTIONr_scangle_it3.3614.54367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 211 -
Rwork0.367 3533 -
obs--99.92 %
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)
15.57453.9959-7.6664.3162-5.73716.1201-0.50780.6017-0.2012-0.68140.2388-0.47360.4790.27240.2689-0.6627-0.06910.0788-0.2223-0.0327-0.340232.758533.167294.9442
21.87620.67441.85664.29783.54318.86680.05020.4493-0.7169-0.28560.1417-0.30961.5420.2475-0.19190.13890.09950.0379-0.2648-0.21150.038333.0553-1.6049327.9356
31.3513-1.5612-1.77072.88493.84649.43910.0282-0.0928-0.1587-0.22620.0307-0.0159-0.2574-0.0675-0.0589-0.59760.124-0.0147-0.31390.0202-0.493933.122126.8611362.5612
44.16971.6524-2.5676.5713-5.57611.0833-0.09-0.3857-0.865-0.04170.83411.05951.4408-2.173-0.7441-0.3839-0.3057-0.03440.16680.21460.05638.502711.5663326.6032
53.5291-0.0087-1.21042.24591.00175.41620.1588-0.29290.49950.26120.0625-0.1782-1.02270.271-0.2213-0.3820.01470.0634-0.34520.044-0.460320.8551.1894334.5708
64.3186-1.55540.78365.5851-1.00055.72330.1145-0.10510.21320.30170.0740.3267-0.41960.3237-0.1885-0.6265-0.10420.0532-0.11790.1352-0.365151.183947.7106319.9231
74.32510.2197-1.15794.614-1.448110.82810.0688-0.09430.219-0.3033-0.0562-0.78270.28991.8829-0.0125-0.42010.18250.06950.20890.0741-0.140473.828720.8182333.892
85.2198-1.94980.25556.0646-0.64936.14910.26520.34250.4441-0.6751-0.30380.525-0.7727-1.08370.0386-0.02020.4672-0.0146-0.08610.0411-0.2828-21.733569.7751355.9964
96.29528.4599-3.949611.7005-4.54934.212-0.08951.11760.5172-0.77780.07920.5266-0.484-0.51610.0103-0.3940.0141-0.0770.0417-0.0321-0.138233.556445.2299305.7347
1012.32379.2171-9.41766.8936-7.04357.1968-0.7791.94310.1231-1.11750.9721-0.27751.1299-2.6605-0.19310.5437-0.055-0.03340.31-0.0264-0.401459.925717.7194316.7934
1110.0276-0.5208-1.96180.0313-0.03364.6748-0.04650.0058-0.3594-1.2433-0.18231.06551.0058-0.44210.2288-0.04990.1736-0.15190.0162-0.0391-0.213653.15512.6331355.8366
1214.5136-16.0469-10.908817.778212.10398.2498-1.14540.2677-1.61221.8915-0.20751.36010.6108-1.2161.3528-0.37390.21540.07440.18740.0026-0.391.303741.8798329.7224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1465 - 146
2X-RAY DIFFRACTION2BB2 - 1462 - 146
3X-RAY DIFFRACTION3CC4 - 1464 - 146
4X-RAY DIFFRACTION4DD4 - 1464 - 146
5X-RAY DIFFRACTION5AA185 - 440185 - 440
6X-RAY DIFFRACTION6BB185 - 440185 - 440
7X-RAY DIFFRACTION7CC185 - 440185 - 440
8X-RAY DIFFRACTION8DD185 - 440185 - 440
9X-RAY DIFFRACTION9AA147 - 172147 - 172
10X-RAY DIFFRACTION10BB147 - 173147 - 173
11X-RAY DIFFRACTION11CC147 - 170147 - 170
12X-RAY DIFFRACTION12DD147 - 174147 - 174

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