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- PDB-1ksy: Crystal Structures of Two Intermediates in the Assembly of the Pa... -

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Basic information

Entry
Database: PDB / ID: 1ksy
TitleCrystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex
Components
  • E1 Recognition Sequence, Strand 1
  • E1 Recognition Sequence, Strand 2
  • REPLICATION PROTEIN E1
KeywordsREPLICATION/DNA / PAPILLOMAVIRUS / DNA-BINDING DOMAIN / REPLICATION / INITIATOR PROTEIN / HELICASE / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


DNA 3'-5' helicase / DNA helicase activity / DNA replication / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Replication Protein E1; Chain: A, - #10 / DNA helicase E1, C-terminal, Papillomavirus / DNA helicase E1, N-terminal, Papillomavirus / Replication protein E1, papillomavirus / DNA helicase E1, DNA-binding domain, papillomavirus / DNA helicase E1, DNA-binding domain superfamily, papillomavirus / Papillomavirus helicase / E1 Protein, N terminal domain / Papillomavirus E1, DNA-binding domain / Replication Protein E1; Chain: A, ...Replication Protein E1; Chain: A, - #10 / DNA helicase E1, C-terminal, Papillomavirus / DNA helicase E1, N-terminal, Papillomavirus / Replication protein E1, papillomavirus / DNA helicase E1, DNA-binding domain, papillomavirus / DNA helicase E1, DNA-binding domain superfamily, papillomavirus / Papillomavirus helicase / E1 Protein, N terminal domain / Papillomavirus E1, DNA-binding domain / Replication Protein E1; Chain: A, / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Replication protein E1
Similarity search - Component
Biological speciesBovine papillomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsEnemark, E.J. / Stenlund, A. / Joshua-Tor, L.
CitationJournal: EMBO J. / Year: 2002
Title: Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex.
Authors: Enemark, E.J. / Stenlund, A. / Joshua-Tor, L.
History
DepositionJan 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
D: E1 Recognition Sequence, Strand 1
E: E1 Recognition Sequence, Strand 1
F: E1 Recognition Sequence, Strand 2
A: REPLICATION PROTEIN E1
B: REPLICATION PROTEIN E1
C: REPLICATION PROTEIN E1


Theoretical massNumber of molelcules
Total (without water)72,0116
Polymers72,0116
Non-polymers00
Water543
1
D: E1 Recognition Sequence, Strand 1
F: E1 Recognition Sequence, Strand 2
A: REPLICATION PROTEIN E1
C: REPLICATION PROTEIN E1


Theoretical massNumber of molelcules
Total (without water)48,0104
Polymers48,0104
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: E1 Recognition Sequence, Strand 1
B: REPLICATION PROTEIN E1

E: E1 Recognition Sequence, Strand 1
B: REPLICATION PROTEIN E1


Theoretical massNumber of molelcules
Total (without water)48,0014
Polymers48,0014
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)149.111, 110.600, 75.084
Angle α, β, γ (deg.)90.00, 116.85, 90.00
Int Tables number5
Space group name H-MC121
DetailsE1 dimerization occurs upon binding to the adjacent sites of the target DNA sequence.

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Components

#1: DNA chain E1 Recognition Sequence, Strand 1


Mass: 6435.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 5'-ATAATTGTTGTTAACAATAAT-3'
#2: DNA chain E1 Recognition Sequence, Strand 2


Mass: 6444.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'-ATTATTGTTAACAACAATTAT-3'
#3: Protein REPLICATION PROTEIN E1


Mass: 17565.467 Da / Num. of mol.: 3 / Fragment: DNA Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine papillomavirus / Plasmid: PET11CGST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03116
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.8 Å3/Da / Density % sol: 67.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MgSO4, spermine tetrahydrochloride, ethylene glycol, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgSO411
2spermine tetrahydrochloride11
3ethylene glycol11
4DTT11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-IDChemical formula
120 mM1reservoirMgSO4
22.5 mM1reservoir
35 %1reservoir
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 14, 2000 / Details: mirrors
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 20851 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.2
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 3.59 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2091 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 72557
Reflection shell
*PLUS
% possible obs: 99.6 % / Num. unique obs: 2091 / Num. measured obs: 6981

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F08

1f08


Resolution: 3.05→35.53 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 244686.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.316 842 4.4 %RANDOM
Rwork0.277 ---
all-20829 --
obs-19115 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.6956 Å2 / ksol: 0.261155 e/Å3
Displacement parametersBiso mean: 68.6 Å2
Baniso -1Baniso -2Baniso -3
1-43.23 Å20 Å20.35 Å2
2---8.97 Å20 Å2
3----34.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a1.01 Å0.87 Å
Refinement stepCycle: LAST / Resolution: 3.05→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 1282 0 3 4795
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
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_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it13.111.5
X-RAY DIFFRACTIONc_mcangle_it19.922
X-RAY DIFFRACTIONc_scbond_it17.942
X-RAY DIFFRACTIONc_scangle_it25.382.5
LS refinement shellResolution: 3.05→3.24 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.48 108 4.1 %
Rwork0.429 2508 -
obs--75.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor obs: 0.2805 / Rfactor Rfree: 0.3172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.93
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.48

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