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- PDB-1a7g: THE CRYSTAL STRUCTURE OF THE E2 DNA-BINDING DOMAIN FROM HUMAN PAP... -

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Basic information

Entry
Database: PDB / ID: 1a7g
TitleTHE CRYSTAL STRUCTURE OF THE E2 DNA-BINDING DOMAIN FROM HUMAN PAPILLOMAVIRUS AT 2.4 ANGSTROMS
ComponentsREGULATORY PROTEIN E2
KeywordsTRANSCRIPTION REGULATION / E2 / PAPILLOMAVIRUS / CERVICAL CANCER
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 speciesHuman papillomavirus type 31
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBussiere, D.E. / Giranda, V.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of the E2 DNA-binding domain from human papillomavirus serotype 31 at 2.4 A.
Authors: Bussiere, D.E. / Kong, X. / Egan, D.A. / Walter, K. / Holzman, T.F. / Lindh, F. / Robins, T. / Giranda, V.L.
History
DepositionMar 13, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: REGULATORY PROTEIN E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5553
Polymers9,3631
Non-polymers1922
Water1,33374
1
E: REGULATORY PROTEIN E2
hetero molecules

E: REGULATORY PROTEIN E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1106
Polymers18,7252
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area2650 Å2
ΔGint-87 kcal/mol
Surface area8630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)45.890, 45.890, 195.636
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11E-2-

SO4

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Components

#1: Protein REGULATORY PROTEIN E2 / E2 DBD


Mass: 9362.728 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 31 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 16 / Strain: SEROTYPE-31 / Cell line: BL21 / Gene: E2 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P17383
#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.: 74 / 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: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-25 mg/mlprotein1drop
2100 mMcitrate1reservoir
345-65 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 5649 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 4
Reflection shellResolution: 2.4→2.6 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.185 / % possible all: 88.4
Reflection
*PLUS
Num. measured all: 60427
Reflection shell
*PLUS
% possible obs: 88.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.85phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BPV-1 STRUCTURE

Resolution: 2.4→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.297 355 8.3 %RANDOM
Rwork0.211 ---
obs0.211 4293 83 %-
Displacement parametersBiso mean: 26.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 0 10 74 742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it22
LS refinement shellResolution: 2.4→2.5 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.316 26 4.2 %
Rwork0.324 343 -
obs--58 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.2

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