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- PDB-1b79: N-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB -

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Basic information

Entry
Database: PDB / ID: 1b79
TitleN-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB
ComponentsDnaB Helicase
KeywordsHYDROLASE / HELICASE / HEXAMER / DNA REPLICATION
Function / homology
Function and homology information


DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer / replisome ...DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer / replisome / response to ionizing radiation / replication fork processing / DNA replication initiation / DNA helicase activity / helicase activity / 5'-3' DNA helicase activity / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol
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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Replicative DNA helicase DnaB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsFass, D. / Bogden, C.E. / Berger, J.M.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of the N-terminal domain of the DnaB hexameric helicase.
Authors: Fass, D. / Bogden, C.E. / Berger, J.M.
History
DepositionJan 28, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DnaB Helicase
B: DnaB Helicase
C: DnaB Helicase
D: DnaB Helicase


Theoretical massNumber of molelcules
Total (without water)52,8914
Polymers52,8914
Non-polymers00
Water77543
1
A: DnaB Helicase


Theoretical massNumber of molelcules
Total (without water)13,2231
Polymers13,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DnaB Helicase


Theoretical massNumber of molelcules
Total (without water)13,2231
Polymers13,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DnaB Helicase


Theoretical massNumber of molelcules
Total (without water)13,2231
Polymers13,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DnaB Helicase


Theoretical massNumber of molelcules
Total (without water)13,2231
Polymers13,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.300, 66.400, 107.000
Angle α, β, γ (deg.)90.00, 93.80, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.768164, 0.638414, -0.048512), (0.639961, 0.763301, -0.088392), (-0.019396, -0.098949, -0.994901)8.9954, 2.1592, 104.5663
2given(-0.873933, -0.031704, 0.485002), (0.028668, -0.9995, -0.013669), (0.485191, 0.001954, 0.874404)-21.1573, 50.4153, 53.5314
3given(-0.647306, 0.623192, 0.438881), (-0.654522, -0.749537, 0.098975), (0.390643, -0.223201, 0.893072)-1.6263, 13.963, 64.4059

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Components

#1: Protein
DnaB Helicase / E.C.3.6.1.-


Mass: 13222.717 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Details: hexamers not associated in crystal / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS
References: UniProt: P0ACB0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.36 Å3/Da / Density % sol: 53 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.9 / Details: pH 6.9, VAPOR DIFFUSION, HANGING DROP
Components of the solutionsName: SODIUM CACODYLATE
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG80001drop
250 mMcacodylate1drop
325 mM1dropMgCl2
416 %PEG80001reservoir
540 mMcacodylate1reservoir
620 mM1reservoirMgCl2
78 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9667
DetectorDate: Feb 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9667 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 21651 / % possible obs: 98.7 % / Redundancy: 3.4 % / Rsym value: 6.9 / Net I/σ(I): 9
Reflection
*PLUS
Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1277 6.7 %RANDOM
Rwork0.263 ---
obs-19127 88.3 %-
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 0 43 3245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.433
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.3833 118
Rwork0.3838 1561

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