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- PDB-1f9f: CRYSTAL STRUCTURE OF THE HPV-18 E2 DNA-BINDING DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1f9f
TitleCRYSTAL STRUCTURE OF THE HPV-18 E2 DNA-BINDING DOMAIN
ComponentsRegulatory protein E2
KeywordsTRANSCRIPTION / Dimeric beta barrel / activator / DNA-binding / trans-acting factor
Function / homology
Function and homology information


host cytoskeleton / viral DNA genome replication / host cell mitochondrial membrane / 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 18
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsKim, S.S. / Tam, J. / Wang, A.F. / Hegde, R.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The structural basis of DNA target discrimination by papillomavirus E2 proteins.
Authors: Kim, S.S. / Tam, J.K. / Wang, A.F. / Hegde, R.S.
History
DepositionJul 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_distant_solvent_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num ..._entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein E2
B: Regulatory protein E2
C: Regulatory protein E2
D: Regulatory protein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5486
Polymers38,3564
Non-polymers1922
Water1,78399
1
A: Regulatory protein E2
B: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)19,1782
Polymers19,1782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-12 kcal/mol
Surface area8130 Å2
MethodPISA
2
C: Regulatory protein E2
D: Regulatory protein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3704
Polymers19,1782
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-44 kcal/mol
Surface area8190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.500, 46.800, 161.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Regulatory protein E2


Mass: 9588.977 Da / Num. of mol.: 4 / Fragment: RESIDUES 287-365 OF HPV-18 E2 WITH GSHM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 18 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 18 / Gene: E2 / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: P06790
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
225 mMTris-HCl1drop
3100 mM1dropNaCl
410 mMdithiothreitol1drop
52.7 Mammonium sulfate1reservoir
60.1 Msodium acetate1reservoir
71

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 21.3 Å2
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 99 Å / Num. obs: 25003 / % possible obs: 97.5 % / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / % possible obs: 88.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→30.52 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 546997.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2367 9.8 %RANDOM
Rwork0.237 ---
obs0.237 24144 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.54 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å20 Å20 Å2
2---0.45 Å20 Å2
3----3.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→30.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 10 99 2560
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.028
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.42
X-RAY DIFFRACTIONc_mcbond_it2.391.5
X-RAY DIFFRACTIONc_mcangle_it3.292
X-RAY DIFFRACTIONc_scbond_it3.62
X-RAY DIFFRACTIONc_scangle_it4.72.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 318 9.3 %
Rwork0.278 3100 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.42

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