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- PDB-1jjh: E2 DNA-binding Domain from Bovine Papillomavirus Type 1 -

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Basic information

Entry
Database: PDB / ID: 1jjh
TitleE2 DNA-binding Domain from Bovine Papillomavirus Type 1
ComponentsREGULATORY PROTEIN E2
KeywordsDNA BINDING PROTEIN / BPV-1 / E2 / DNA-binding domain
Function / homology
Function and homology information


viral DNA genome replication / regulation of DNA replication / DNA replication / DNA-binding transcription factor activity / nucleotide binding / DNA-templated transcription / host cell nucleus / DNA binding
Similarity search - Function
Papillomavirus E2, C-terminal / Papillomavirus E2, N-terminal / Regulatory protein E2 / E2 regulatory, transactivation domain / E2 regulatory, transactivation domain, subdomain 1 / E2 regulatory, transactivation domain, subdomain 2 / E2 (early) protein, N terminal / E2 (early) protein, C terminal / E2/EBNA1, C-terminal / RRM (RNA recognition motif) domain ...Papillomavirus E2, C-terminal / Papillomavirus E2, N-terminal / Regulatory protein E2 / E2 regulatory, transactivation domain / E2 regulatory, transactivation domain, subdomain 1 / E2 regulatory, transactivation domain, subdomain 2 / E2 (early) protein, N terminal / E2 (early) protein, C terminal / E2/EBNA1, C-terminal / RRM (RNA recognition motif) domain / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulatory protein E2
Similarity search - Component
Biological speciesBovine papillomavirus type 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHegde, R.S. / Wang, A.F. / Kim, S.S. / Schapira, M.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Subunit rearrangement accompanies sequence-specific DNA binding by the bovine papillomavirus-1 E2 protein.
Authors: Hegde, R.S. / Wang, A.F. / Kim, S.S. / Schapira, M.
History
DepositionJul 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 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: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REGULATORY PROTEIN E2
B: REGULATORY PROTEIN E2
C: REGULATORY PROTEIN E2


Theoretical massNumber of molelcules
Total (without water)29,0763
Polymers29,0763
Non-polymers00
Water1,11762
1
A: REGULATORY PROTEIN E2

A: REGULATORY PROTEIN E2


Theoretical massNumber of molelcules
Total (without water)19,3842
Polymers19,3842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
2
B: REGULATORY PROTEIN E2

B: REGULATORY PROTEIN E2


Theoretical massNumber of molelcules
Total (without water)19,3842
Polymers19,3842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
3
C: REGULATORY PROTEIN E2

C: REGULATORY PROTEIN E2


Theoretical massNumber of molelcules
Total (without water)19,3842
Polymers19,3842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)122.290, 122.290, 85.019
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Detailsthe biological assembly is a homodimer

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Components

#1: Protein REGULATORY PROTEIN E2


Mass: 9691.965 Da / Num. of mol.: 3 / Fragment: DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine papillomavirus type 1 / Genus: Deltapapillomavirus / Species: Bovine papillomavirus - 1 / Gene: E2 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BD21(DE3) / References: UniProt: P03122
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: ammonium sulfate, imidazole, magnesium chloride, glycerol, DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
20.5-0.6 Mammonium sulfate1drop
325 mMimidazole1drop
41 mM1dropMgCl2
55 %(v/v)glycerol1drop
65 mg/mldithiothreitol1drop
71.1-1.3 Mammonium sulfate1reservoir
850 mMimidazole1reservoir
92 mM1reservoirMgCl2
1010 %glycerol1reservoir
1110 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.14
Reflection
*PLUS
Lowest resolution: 50 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 185476.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1036 10.2 %RANDOM
Rwork0.225 ---
obs0.225 10125 75.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 95.3039 Å2 / ksol: 0.641847 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.65 Å24.33 Å20 Å2
2---4.65 Å20 Å2
3---9.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 0 62 1896
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it3.172
X-RAY DIFFRACTIONc_scangle_it4.112.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 130 10.6 %
Rwork0.231 1096 -
obs-1096 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 10.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
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: 0.291 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.231

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