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- PDB-3mi7: An Enhanced Repressor of Human Papillomavirus E2 Protein -

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Basic information

Entry
Database: PDB / ID: 3mi7
TitleAn Enhanced Repressor of Human Papillomavirus E2 Protein
ComponentsRegulatory protein E2
KeywordsVIRAL PROTEIN / papillomavirus DNA-binding domain / beta-barrel
Function / homology
Function and homology information


host cytoskeleton / 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 speciesHuman papillomavirus type 16
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBohm, A. / Baleja, J. / Bose, K. / Meinke, G.
CitationJournal: Faseb J. / Year: 2011
Title: Design and characterization of an enhanced repressor of human papillomavirus E2 protein.
Authors: Bose, K. / Meinke, G. / Bohm, A. / Baleja, J.D.
History
DepositionApr 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Oct 6, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Regulatory protein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1487
Polymers9,7751
Non-polymers3726
Water1,29772
1
X: Regulatory protein E2
hetero molecules

X: Regulatory protein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,29514
Polymers19,5502
Non-polymers74512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3360 Å2
ΔGint4 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.860, 43.099, 45.666
Angle α, β, γ (deg.)90.00, 120.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Regulatory protein E2


Mass: 9775.230 Da / Num. of mol.: 1 / Fragment: UNP residues 283-365 / Mutation: H290E, C309S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16 / Strain: Type 16 / Gene: E2 / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P03120
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM sodium citrate, 100 mM ammonium acetate, 10% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Oct 31, 2008 / Details: mirrors
RadiationMonochromator: multi layer x-ray optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→21.9 Å / Num. obs: 4793 / % possible obs: 95.38 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.077 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 712 / Rsym value: 0.282 / % possible all: 93.1

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Processing

Software
NameVersionClassification
CrysalisProdata collection
AMoREphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BY9

1by9


Resolution: 2.2→33.07 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.875 / SU B: 14.329 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28054 229 4.6 %RANDOM
Rwork0.18351 ---
obs0.1878 4702 95.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.984 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.13 Å2
2--0.06 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms642 0 24 72 738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022687
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.931924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.027583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55922.825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89415115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.054153
X-RAY DIFFRACTIONr_chiral_restr0.1070.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021480
X-RAY DIFFRACTIONr_mcbond_it0.6761.5408
X-RAY DIFFRACTIONr_mcangle_it1.2982666
X-RAY DIFFRACTIONr_scbond_it2.0053279
X-RAY DIFFRACTIONr_scangle_it3.2124.5256
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 14 -
Rwork0.266 358 -
obs--94.42 %
Refinement TLS params.Method: refined / Origin x: 19.3908 Å / Origin y: 0.8093 Å / Origin z: 30.1675 Å
111213212223313233
T0.0095 Å2-0.0034 Å20.0196 Å2-0.0407 Å20.0057 Å2--0.0549 Å2
L2.402 °2-1.112 °21.1576 °2-2.8878 °20.6092 °2--4.6339 °2
S-0.0231 Å °-0.111 Å °0.0299 Å °0.073 Å °-0.0828 Å °0.015 Å °0.0132 Å °-0.0796 Å °0.1059 Å °

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