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- PDB-1r9w: Crystal Structure of the DNA-binding domain of the human papillom... -

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Basic information

Entry
Database: PDB / ID: 1r9w
TitleCrystal Structure of the DNA-binding domain of the human papillomavirus type 18 (HPV-18) replication initiation protein E1
ComponentsReplication protein E1
KeywordsREPLICATION / HPV-18 / papillomavirus / DNA-binding domain / viral replication / initiator protein
Function / homology
Function and homology information


DNA 3'-5' helicase / DNA helicase activity / viral genome replication / host cell cytoplasm / 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
Replication protein E1
Similarity search - Component
Biological speciesHuman papillomavirus type 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAuster, A.S. / Joshua-Tor, L.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The DNA-binding domain of human papillomavirus type 18 E1. Crystal structure, dimerization, and DNA binding.
Authors: Auster, A.S. / Joshua-Tor, L.
History
DepositionOct 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication protein E1


Theoretical massNumber of molelcules
Total (without water)16,3351
Polymers16,3351
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.540, 46.240, 43.190
Angle α, β, γ (deg.)90.00, 94.01, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer. There is one monomer in the asymmetric unit.

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Components

#1: Protein Replication protein E1


Mass: 16335.233 Da / Num. of mol.: 1 / Fragment: DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 18 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 18 / Gene: E1
Plasmid details: constructed with a glutathione S-transferase (GST) cassette and a thrombin cleavage site
Plasmid: pET11C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P06789
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, ammonium acetate, sodium citrate, DTT, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 mMHEPES1droppH7.5
3100 mM1dropNaCl
410 mMdithiothreitol1drop
528-30 %PEG40001reservoir
6100 mMammonium acetate1reservoir
7100 mMsodium citrate1reservoirpH5.0-5.6
850-100 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 12094 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 3.41 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.25 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1412 / % possible all: 69.1
Reflection
*PLUS
% possible obs: 93 % / Num. measured all: 45127
Reflection shell
*PLUS
% possible obs: 69.1 % / Num. unique obs: 1412

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F08 with non-identical residues mutated to alanines, and no solvent

1f08


Resolution: 1.8→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Deposited structure factor file includes data to 1.5 A, however, statistics and refinement are reported to 1.8 A.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 599 -random
Rwork0.213 ---
all-12094 --
obs-11495 93 %-
Displacement parametersBiso mean: 19.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 0 109 1213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.04
RfactorNum. reflection% reflection
Rfree0.343 73 -
Rwork0.23 --
obs-1412 69.1 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

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