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

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Basic information

Entry
Database: PDB / ID: 1ksx
TitleCrystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex
Components
  • E1 Recognition Sequence
  • REPLICATION PROTEIN E1DNA replication
KeywordsREPLICATION/DNA / PAPILLOMAVIRUS / DNA-BINDING DOMAIN / REPLICATION / INITIATOR PROTEIN / HELICASE / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


DNA helicase activity / DNA helicase / 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: 3.2 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
C: E1 Recognition Sequence
G: E1 Recognition Sequence
K: E1 Recognition Sequence
O: E1 Recognition Sequence
A: REPLICATION PROTEIN E1
B: REPLICATION PROTEIN E1
E: REPLICATION PROTEIN E1
F: REPLICATION PROTEIN E1
I: REPLICATION PROTEIN E1
J: REPLICATION PROTEIN E1
M: REPLICATION PROTEIN E1
N: REPLICATION PROTEIN E1


Theoretical massNumber of molelcules
Total (without water)160,79912
Polymers160,79912
Non-polymers00
Water36020
1
C: E1 Recognition Sequence
G: E1 Recognition Sequence
A: REPLICATION PROTEIN E1
B: REPLICATION PROTEIN E1
E: REPLICATION PROTEIN E1
F: REPLICATION PROTEIN E1


Theoretical massNumber of molelcules
Total (without water)80,4006
Polymers80,4006
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: E1 Recognition Sequence
O: E1 Recognition Sequence
I: REPLICATION PROTEIN E1
J: REPLICATION PROTEIN E1
M: REPLICATION PROTEIN E1
N: REPLICATION PROTEIN E1


Theoretical massNumber of molelcules
Total (without water)80,4006
Polymers80,4006
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.246, 103.650, 124.996
Angle α, β, γ (deg.)90.00, 99.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsE1 multimerization occurs upon binding to the adjacent sites of the target DNA sequence.

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Components

#1: DNA chain
E1 Recognition Sequence


Mass: 6444.222 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
REPLICATION PROTEIN E1 / DNA replication


Mass: 16877.770 Da / Num. of mol.: 8 / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ca(CF3COO)2, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ca(CF3COO)211
2DTT11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mM1reservoirMgSO4
22.5 mMspermine tetrahydrochloride1reservoir
35 %ethylene glycol1reservoir

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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: Nov 4, 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: 3.2→50 Å / Num. all: 35201 / Num. obs: 35038 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.195 / Net I/σ(I): 9.14
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3474 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 125960
Reflection shell
*PLUS
% possible obs: 99.3 % / Num. unique obs: 3474 / Num. measured obs: 12242

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F08

1f08


Resolution: 3.2→42.62 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 130431.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT IS LESS THAN SPECIFIED IN REMARK 3. THE VALUES LISTED IN REMARK 3 ARE 4-FOLD GREATER (REFLECTING THE 4-FOLD STRICT NCS). 2328 PROTEIN ...Details: THE NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT IS LESS THAN SPECIFIED IN REMARK 3. THE VALUES LISTED IN REMARK 3 ARE 4-FOLD GREATER (REFLECTING THE 4-FOLD STRICT NCS). 2328 PROTEIN ATOMS, 428 NUCLEIC ACID ATOMS, AND 5 SOLVENT ATOMS WERE USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1612 5.1 %RANDOM
Rwork0.263 ---
all-35201 --
obs-31865 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.0378 Å2 / ksol: 0.240909 e/Å3
Displacement parametersBiso mean: 59.5 Å2
Baniso -1Baniso -2Baniso -3
1-31.6 Å20 Å212.57 Å2
2---16.2 Å20 Å2
3----15.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a1 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 3.2→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9312 1712 0 20 11044
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it10.221.5
X-RAY DIFFRACTIONc_mcangle_it15.212
X-RAY DIFFRACTIONc_scbond_it17.42
X-RAY DIFFRACTIONc_scangle_it24.342.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.429 237 5.1 %
Rwork0.382 4449 -
obs--80.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 50 Å / Rfactor obs: 0.2634 / Rfactor Rfree: 0.2844
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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