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- PDB-1f08: CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF THE REPLICATION IN... -

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Basic information

Entry
Database: PDB / ID: 1f08
TitleCRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF THE REPLICATION INITIATION PROTEIN E1 FROM PAPILLOMAVIRUS
ComponentsREPLICATION PROTEIN E1DNA replication
KeywordsREPLICATION / Papillomavirus / DNA-binding domain / initiator protein / helicase
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
BROMIDE ION / Replication protein E1
Similarity search - Component
Biological speciesBovine papillomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsEnemark, E.J. / Chen, G. / Vaughn, D.E. / Stenlund, A. / Joshua-Tor, L.
CitationJournal: Mol.Cell / Year: 2000
Title: Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus.
Authors: Enemark, E.J. / Chen, G. / Vaughn, D.E. / Stenlund, A. / Joshua-Tor, L.
History
DepositionMay 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REPLICATION PROTEIN E1
B: REPLICATION PROTEIN E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,87416
Polymers33,7562
Non-polymers1,11914
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.170, 84.897, 124.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsIn the absence of DNA, the protein is monomeric in solution. In the presence of DNA, the biologically relevant oligomerization state is a dimer. In this entry the two chains are in the the correct DNA-binding dimeric orientation.

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Components

#1: Protein REPLICATION PROTEIN E1 / DNA replication


Mass: 16877.770 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine papillomavirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03116
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, pH 6.5, NaBr or NaCl, 8 mg/mL protein, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 8 mg/ml / Common name: protein

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X26C11.1
SYNCHROTRONNSLS X8C20.979
Detector
TypeIDDetectorDate
MARRESEARCH1CCDOct 26, 1999
MARRESEARCH2CCDMay 31, 1999
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.9791
ReflectionResolution: 1.9→50 Å / Num. all: 36016 / Num. obs: 35804 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 9.28 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.05 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 4.35 / Num. unique all: 3500 / % possible all: 96.4
Reflection
*PLUS
Num. measured all: 332339
Reflection shell
*PLUS
% possible obs: 96.4 % / Num. unique obs: 3500 / Num. measured obs: 21175

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Processing

Software
NameClassification
SnBphasing
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→25 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 368558.09 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1668 5 %Random
Rwork0.241 ---
all-33605 --
obs-33605 93.3 %-
Solvent computationSolvent model: flat model / Bsol: 50.5091 Å2 / ksol: 0.347299 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å20 Å2
2---13.397 Å20 Å2
3---10.837 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 14 100 2463
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.61
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.2261.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it1.7872
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.337 149 5.4 %
Rwork0.301 2621 -
obs--78.5 %
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
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.337 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.301 / Rfactor obs: 0.303

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