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- PDB-3bh0: ATPase Domain of G40P -

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Basic information

Entry
Database: PDB / ID: 3bh0
TitleATPase Domain of G40P
ComponentsDNAB-LIKE REPLICATIVE HELICASE
KeywordsREPLICATION / Helicase / ATPase
Function / homology
Function and homology information


double-stranded DNA helicase activity / DNA unwinding involved in DNA replication / DNA helicase / hydrolase 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus phage SPP1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.35 Å
AuthorsWang, G. / Klein, M.G. / Tokonzaba, E. / Zhang, Y. / Holden, L.G. / Chen, X.S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: The structure of a DnaB-family replicative helicase and its interactions with primase.
Authors: Wang, G. / Klein, M.G. / Tokonzaba, E. / Zhang, Y. / Holden, L.G. / Chen, X.S.
History
DepositionNov 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNAB-LIKE REPLICATIVE HELICASE


Theoretical massNumber of molelcules
Total (without water)35,5241
Polymers35,5241
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.779, 96.779, 54.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein DNAB-LIKE REPLICATIVE HELICASE


Mass: 35524.035 Da / Num. of mol.: 1 / Fragment: G40P ATPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPP1 (virus) / Genus: Lambda-like viruses / Production host: Escherichia coli (E. coli) / References: UniProt: Q38152
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate (pH 5.6), 8-12% PEG-4000, 0.2 M ammonium acetate, 1 mM ATP-gamma-S, VAPOR DIFFUSION, HANGING DROP, temperature 100K, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.35→85 Å / Num. all: 12256 / Num. obs: 12256 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.032 / Rsym value: 0.0364 / Net I/σ(I): 43
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 6 / Num. unique all: 1186 / Rsym value: 0.364 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.166 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.542 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2851 599 4.9 %RANDOM
Rwork0.23814 ---
obs0.2403 11627 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.199 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 0 26 2279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9643066
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.28724.779113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.19115442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.0641519
X-RAY DIFFRACTIONr_chiral_restr0.1150.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021703
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.2965
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21539
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4480.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6951.51455
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21622271
X-RAY DIFFRACTIONr_scbond_it1.4423929
X-RAY DIFFRACTIONr_scangle_it2.434.5795
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 51 -
Rwork0.328 831 -
obs--99.89 %

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