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- PDB-2r6a: Crystal Form BH1 -

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Basic information

Entry
Database: PDB / ID: 2r6a
TitleCrystal Form BH1
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 primase activity / DNA replication, synthesis of primer / DNA helicase activity / DNA-directed RNA polymerase complex / DNA helicase / ATP hydrolysis activity / DNA binding / zinc ion binding ...DNA primase DnaG / primosome complex / DNA primase activity / DNA replication, synthesis of primer / DNA helicase activity / DNA-directed RNA polymerase complex / DNA helicase / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / identical protein binding
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, CHC2-type zinc finger / DNA primase, catalytic core, N-terminal domain superfamily / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / Toprim-like / 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 / Toprim domain profile. / TOPRIM domain / Helix Hairpins / Helix non-globular / Special / 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 / DNA primase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 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 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replicative helicase
B: Replicative helicase
C: DnaG Primase, Helicase Binding Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,5807
Polymers118,1953
Non-polymers3844
Water54030
1
A: Replicative helicase
B: Replicative helicase
C: DnaG Primase, Helicase Binding Domain
hetero molecules

A: Replicative helicase
B: Replicative helicase
C: DnaG Primase, Helicase Binding Domain
hetero molecules

A: Replicative helicase
B: Replicative helicase
C: DnaG Primase, Helicase Binding Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,73921
Polymers354,5869
Non-polymers1,15312
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area40570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.751, 226.751, 75.902
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEGLUAA9 - 919 - 91
21ILEGLUBB9 - 919 - 91
12LEUSERAA92 - 15192 - 151
22LEUSERBB92 - 15192 - 151
13ILELEUAA183 - 441183 - 441
23ILELEUBB183 - 441183 - 441

NCS ensembles :
ID
1
2
3
DetailsBiological hexamer is generated when the following operators are applied to the au: (x, y, z) (1-y,x-y,z) (y-x+1,1-x,z)

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Components

#1: Protein Replicative helicase / DnaB Helicase


Mass: 50699.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DnaB / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 1 / Fragment: Helicase Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DnaG / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9X4D0, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 30 / 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: 4.76 Å3/Da / Density % sol: 74.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 1.0M Lithium Sulfate, 5% MPD, pH 6.0, 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 315 / Detector: CCD / Date: May 24, 2006
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: 2.9→49.88 Å / Num. all: 49653 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rsym value: 0.07 / Net I/σ(I): 22.32
Reflection shellResolution: 2.9→3 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.87 / Num. unique all: 4947 / % possible all: 99.9

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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: 2.9→49.88 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.884 / SU B: 29.979 / SU ML: 0.275 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.492 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29728 2517 5.1 %RANDOM
Rwork0.25894 ---
all0.2608 47117 --
obs0.2608 47117 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.544 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.3 Å20 Å2
2--0.6 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7302 0 20 30 7352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227403
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9819998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4485925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.04724.32338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.812151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4811564
X-RAY DIFFRACTIONr_chiral_restr0.1010.21173
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025458
X-RAY DIFFRACTIONr_nbd_refined0.2190.23444
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.24
X-RAY DIFFRACTIONr_mcbond_it1.6931.54829
X-RAY DIFFRACTIONr_mcangle_it2.55627493
X-RAY DIFFRACTIONr_scbond_it2.53422879
X-RAY DIFFRACTIONr_scangle_it3.7912.52505
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1332medium positional0.170.5
2236medium positional0.50.5
3828medium positional0.340.5
1296loose positional0.535
2228loose positional0.955
3758loose positional0.815
1332medium thermal0.882
2236medium thermal0.732
3828medium thermal0.532
1296loose thermal2.5610
2228loose thermal2.910
3758loose thermal210
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 177 -
Rwork0.324 3431 -
obs--99.15 %
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)
14.2427-2.0854-1.37864.80212.12433.035-0.0148-0.1222-0.2659-0.0241-0.0328-0.13140.2516-0.15920.0477-0.52920.2034-0.1013-0.5210.0955-0.466775.5299102.151733.6062
20.85580.75520.138513.982-0.0961.7743-0.1690.339-0.2016-0.64950.2161.02440.6848-0.3397-0.047-0.22520.2456-0.0654-0.3530.0081-0.256879.015281.728427.1547
35.13212.8596-0.27372.8029-0.99581.6666-0.23330.3999-0.0152-0.39290.1637-0.29540.13760.48760.06960.10450.11620.00350.25090.0994-0.1992111.089107.8553-15.2041
45.62850.68470.77183.2556-0.18667.0541-0.09820.2713-0.2543-0.37190.04360.11950.28520.05180.0546-0.2240.19820.00260.04550.0951-0.2587106.5378104.9688-2.9127
58.43660.4448-0.67491.3265-0.60913.17990.22280.1576-0.4112-0.0581-0.141-0.14450.27230.5116-0.0818-0.43670.2883-0.0468-0.30720.0419-0.4375104.859298.756229.1212
610.2651-5.8615-0.22223.4997-0.02390.15380.52350.7372-0.3234-0.8386-0.48180.0977-0.0546-0.0654-0.0417-0.35690.1671-0.04620.0832-0.0011-0.3041125.832693.755226.0676
76.0638-5.5269-1.66935.58792.07511.5901-0.19760.54660.32250.1712-0.1938-0.24620.1476-0.23380.3914-0.0107-0.13190.23380.22290.17430.0009149.812188.4321-12.269
82.9522-1.08490.56764.6995-0.01025.71-0.12970.26340.3127-0.15160.04170.5009-0.7712-1.00160.08790.08660.15810.20120.3880.12180.0889143.591288.6283-4.9948
96.72151.08921.12486.59071.77585.43070.13030.05990.95030.1228-0.1008-0.6338-0.48031.3965-0.0295-0.0916-0.0979-0.00180.08210.09960.0878113.8982125.686539.1384
1012.16280.1586-2.27142.44420.47673.55740.4152-0.65910.98560.1239-0.234-0.8118-0.93630.785-0.1812-0.16160.1353-0.1057-0.3516-0.0276-0.138181.0253118.540442.7501
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 91
2X-RAY DIFFRACTION2A92 - 151
3X-RAY DIFFRACTION3A161 - 175
4X-RAY DIFFRACTION3A244 - 286
5X-RAY DIFFRACTION4A287 - 441
6X-RAY DIFFRACTION5B9 - 91
7X-RAY DIFFRACTION6B92 - 151
8X-RAY DIFFRACTION7B155 - 174
9X-RAY DIFFRACTION7B244 - 286
10X-RAY DIFFRACTION8B287 - 441
11X-RAY DIFFRACTION9C461 - 555
12X-RAY DIFFRACTION10C556 - 593

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