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- PDB-2ayg: Crystal structure of HPV6a E2 DNA binding domain bound to an 18 b... -

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Basic information

Entry
Database: PDB / ID: 2ayg
TitleCrystal structure of HPV6a E2 DNA binding domain bound to an 18 base pair DNA target
Components
  • 5'-D(*GP*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*GP*C)-3'
  • Regulatory protein E2
KeywordsTRANSCRIPTION/DNA / beta barrel / double helix / protein-DNA complex / TRANSCRIPTION-DNA COMPLEX
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
DNA / DNA (> 10) / Regulatory protein E2
Similarity search - Component
Biological speciesHuman papillomavirus type 6a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHooley, E. / Brady, R.L. / Gaston, K.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein.
Authors: Hooley, E. / Fairweather, V. / Clarke, A.R. / Gaston, K. / Brady, R.L.
History
DepositionSep 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*GP*C)-3'
D: 5'-D(*GP*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*GP*C)-3'
A: Regulatory protein E2
B: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)31,5154
Polymers31,5154
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.449, 73.449, 109.237
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUAC283 - 3033 - 23
21ALAALALEULEUBD283 - 3033 - 23
32ARGARGTRPTRPAC307 - 31928 - 40
42ARGARGTRPTRPBD307 - 31928 - 40
53ALAALAPHEPHEAC329 - 36050 - 81
63ALAALAPHEPHEBD329 - 36050 - 81
74HISHISLEULEUAC364 - 36685 - 87
84HISHISLEULEUBD364 - 36685 - 87
Detailsbiological assembly is a protein dimer bound to double stranded DNA

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Components

#1: DNA chain 5'-D(*GP*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*GP*C)-3'


Mass: 5516.579 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Regulatory protein E2


Mass: 10240.854 Da / Num. of mol.: 2 / Fragment: C terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 6a / Genus: Alphapapillomavirus / Species: Human papillomavirus - 6 / Gene: E2 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q84294
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.7 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium chloride, Hepes, ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium chloride11
2Hepes11
3ammonium sulphate11
4H2O11
5sodium chloride12
6Hepes12
7ammonium sulphate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2005 / Details: mirrors
RadiationMonochromator: Si Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3.1→63.63 Å / Num. all: 5807 / Num. obs: 6087 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 17.9
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 4.2 / Num. unique all: 429 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1JJ4

1jj4


Resolution: 3.1→63.63 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.875 / SU B: 28.744 / SU ML: 0.476 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.557 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 278 4.6 %RANDOM
Rwork0.203 ---
all0.206 5807 --
obs0.247 6085 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.548 Å2
Baniso -1Baniso -2Baniso -3
1-4.17 Å22.08 Å20 Å2
2--4.17 Å20 Å2
3----6.25 Å2
Refinement stepCycle: LAST / Resolution: 3.1→63.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 732 0 19 2195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212305
X-RAY DIFFRACTIONr_angle_refined_deg2.3222.3333275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg125172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46922.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.03215254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4691510
X-RAY DIFFRACTIONr_chiral_restr0.260.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021498
X-RAY DIFFRACTIONr_nbd_refined0.2780.21231
X-RAY DIFFRACTIONr_nbtor_refined0.3250.21439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.268
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0290.23
X-RAY DIFFRACTIONr_mcbond_it0.7441.5890
X-RAY DIFFRACTIONr_mcangle_it1.37621429
X-RAY DIFFRACTIONr_scbond_it1.20331830
X-RAY DIFFRACTIONr_scangle_it2.0854.51846
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 588 / Refine-ID: X-RAY DIFFRACTION

RmsTypeWeight
0.04TIGHT POSITIONAL0.05
0.09TIGHT THERMAL0.5
LS refinement shellResolution: 3.102→3.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 15 -
Rwork0.321 429 -
obs--99.33 %

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