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- PDB-1ka8: Crystal Structure of the Phage P4 Origin-Binding Domain -

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Basic information

Entry
Database: PDB / ID: 1ka8
TitleCrystal Structure of the Phage P4 Origin-Binding Domain
Componentsputative P4-specific DNA primase
KeywordsTRANSFERASE / winged helix
Function / homology
Function and homology information


DNA primase activity / DNA helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA helicase / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
Toprim domain / D5 N terminal like / Bacteriophage T7, Gp4, DNA primase/helicase, N-terminal / Zinc-binding domain of primase-helicase / Zinc-binding domain of primase-helicase / Archaeal primase DnaG/twinkle-like, TOPRIM domain / DNA primase/nucleoside triphosphatase, C-terminal / Poxvirus D5 protein-like / Bacteriophage/plasmid primase, P4, C-terminal / D5 N terminal like ...Toprim domain / D5 N terminal like / Bacteriophage T7, Gp4, DNA primase/helicase, N-terminal / Zinc-binding domain of primase-helicase / Zinc-binding domain of primase-helicase / Archaeal primase DnaG/twinkle-like, TOPRIM domain / DNA primase/nucleoside triphosphatase, C-terminal / Poxvirus D5 protein-like / Bacteriophage/plasmid primase, P4, C-terminal / D5 N terminal like / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / TOPRIM / Toprim domain profile. / TOPRIM domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative P4-specific DNA primase
Similarity search - Component
Biological speciesEnterobacteria phage P4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.95 Å
AuthorsYeo, H.J. / Ziegelin, G. / Korolev, S. / Calendar, R. / Lanka, E. / Waksman, G.
CitationJournal: Mol.Microbiol. / Year: 2002
Title: Phage P4 origin-binding domain structure reveals a mechanism for regulation of DNA-binding activity by homo- and heterodimerization of winged helix proteins.
Authors: Yeo, H.J. / Ziegelin, G. / Korolev, S. / Calendar, R. / Lanka, E. / Waksman, G.
History
DepositionOct 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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: putative P4-specific DNA primase
B: putative P4-specific DNA primase
C: putative P4-specific DNA primase
D: putative P4-specific DNA primase
E: putative P4-specific DNA primase
F: putative P4-specific DNA primase


Theoretical massNumber of molelcules
Total (without water)69,8486
Polymers69,8486
Non-polymers00
Water21612
1
A: putative P4-specific DNA primase
B: putative P4-specific DNA primase


Theoretical massNumber of molelcules
Total (without water)23,2832
Polymers23,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-13 kcal/mol
Surface area10550 Å2
MethodPISA
2
C: putative P4-specific DNA primase
D: putative P4-specific DNA primase


Theoretical massNumber of molelcules
Total (without water)23,2832
Polymers23,2832
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-11 kcal/mol
Surface area10560 Å2
MethodPISA
3
E: putative P4-specific DNA primase
F: putative P4-specific DNA primase


Theoretical massNumber of molelcules
Total (without water)23,2832
Polymers23,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-14 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.549, 82.549, 232.629
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
putative P4-specific DNA primase


Mass: 11641.309 Da / Num. of mol.: 6 / Fragment: origin-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P4 (virus) / Genus: P2-like viruses / Production host: Escherichia coli (E. coli)
References: UniProt: P10277, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.27 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: ammonium sulfate, sodium citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: used macroseeding / PH range low: 5 / PH range high: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium citrate1reservoirpH4.5-5.0
21.5-1.7 Mammonium sulfate1reservoir
312 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9795, 0.9537
DetectorDetector: CCD / Date: Feb 16, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97951
30.95371
Reflection shellResolution: 2.95→3.06 Å / Rsym value: 0.259 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.95 Å / Lowest resolution: 30 Å / % possible obs: 99 % / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.95→28.35 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1666006.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 927 5 %RANDOM
Rwork0.241 ---
obs0.241 18665 92.8 %-
all-19799 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1963 Å2 / ksol: 0.379888 e/Å3
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.95→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4874 0 0 12 4886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.15
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.95→3.13 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 130 5 %
Rwork0.305 2473 -
obs--79.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.237 / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15
LS refinement shell
*PLUS
Rfactor Rfree: 0.36 / Rfactor Rwork: 0.305

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