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- PDB-2vyf: Crystal Structure of the DnaC -

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Basic information

Entry
Database: PDB / ID: 2vyf
TitleCrystal Structure of the DnaC
ComponentsREPLICATIVE DNA HELICASE
KeywordsHYDROLASE / DNA REPLICATION / NUCLEOTIDE-BINDING / DNAC / HELICASE / ATP-BINDING
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
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 / 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
Similarity search - Component
Biological speciesGEOBACILLUS KAUSTOPHILUS HTA426 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.6 Å
AuthorsLo, Y.H. / Tsai, K.L. / Sun, Y.J. / Hsiao, C.D.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The Crystal Structure of a Replicative Hexameric Helicase Dnac and its Complex with Single-Stranded DNA.
Authors: Lo, Y.H. / Tsai, K.L. / Sun, Y.J. / Chen, W.T. / Huang, C.Y. / Hsiao, C.D.
History
DepositionJul 23, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REPLICATIVE DNA HELICASE
B: REPLICATIVE DNA HELICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4516
Polymers101,6632
Non-polymers7884
Water0
1
A: REPLICATIVE DNA HELICASE
B: REPLICATIVE DNA HELICASE
hetero molecules

A: REPLICATIVE DNA HELICASE
B: REPLICATIVE DNA HELICASE
hetero molecules

A: REPLICATIVE DNA HELICASE
B: REPLICATIVE DNA HELICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,35318
Polymers304,9906
Non-polymers2,36412
Water0
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 area31170 Å2
ΔGint-219.1 kcal/mol
Surface area135870 Å2
MethodPQS
Unit cell
Length a, b, c (Å)176.968, 176.968, 108.824
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein REPLICATIVE DNA HELICASE / DNAC


Mass: 50831.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS KAUSTOPHILUS HTA426 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q5KU75, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Au

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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: 5.91 Å3/Da / Density % sol: 79.02 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→30 Å / Num. obs: 18502 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.4
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.2 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CNS1.2refinement
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3.6→24.87 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE RESIDUES IN CHAIN A INCLUDING 1- 7, 258-264, 365-381, 400-409,AND 436-454 WERE MISSING. THE RESIDUES IN CHAIN B INCLUDING 1-6, 155-157, 179-182, 322-331, 365-381, 397-410 AND 426-454 WERE MISSING.
RfactorNum. reflection% reflectionSelection details
Rfree0.324 1447 7.8 %RANDOM
Rwork0.293 ---
obs0.293 18500 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 104.75 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 167.6 Å2
Baniso -1Baniso -2Baniso -3
1--27.14 Å20 Å20 Å2
2---27.14 Å20 Å2
3---54.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.77 Å0.67 Å
Luzzati d res low-6 Å
Luzzati sigma a1.04 Å0.78 Å
Refinement stepCycle: LAST / Resolution: 3.6→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5942 0 4 0 5946
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.6→3.83 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6 /
Rfactor% reflection
Rfree0.45 8 %
Rwork0.431 -
obs-52.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMDNA-RNA.TOP

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