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- PDB-2r6e: Crystal Form B2 -

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Basic information

Entry
Database: PDB / ID: 2r6e
TitleCrystal Form B2
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
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replicative DNA helicase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 5.019 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: Version format compliance
Revision 1.2Feb 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

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Assembly

Deposited unit
A: Replicative helicase
B: Replicative helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5914
Polymers101,3992
Non-polymers1922
Water0
1
A: Replicative helicase
B: Replicative helicase
hetero molecules

A: Replicative helicase
B: Replicative helicase
hetero molecules

A: Replicative helicase
B: Replicative helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,77312
Polymers304,1976
Non-polymers5766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPISA
Unit cell
Length a, b, c (Å)199.797, 199.797, 195.036
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: 2.5M Sodium Chloride, pH 7.0, VAPOR DIFFUSION

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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
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 5→25 Å / Num. obs: 6233 / % possible obs: 95.8 % / Observed criterion σ(I): 1 / Redundancy: 10.2 % / Rsym value: 0.058 / Net I/σ(I): 35.9
Reflection shellResolution: 5→5.18 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 471 / Rsym value: 0.533 / % possible all: 74.5

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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: 5.019→20 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.866 / SU B: 492.884 / SU ML: 4.486 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.056 / ESU R Free: 2.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.3972 297 4.8 %RANDOM
Rwork0.39341 ---
all0.39358 5879 --
obs0.39358 5879 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.031 Å2
Baniso -1Baniso -2Baniso -3
1--35.72 Å2-17.86 Å20 Å2
2---35.72 Å20 Å2
3---53.58 Å2
Refinement stepCycle: LAST / Resolution: 5.019→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 0 10 0 5990
LS refinement shellResolution: 5.019→5.141 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.491 20 -
Rwork0.483 310 -
obs--73.83 %

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