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- PDB-2q79: Crystal Structure of single chain E2C from HPV16 with a 12aa link... -

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Basic information

Entry
Database: PDB / ID: 2q79
TitleCrystal Structure of single chain E2C from HPV16 with a 12aa linker for monomerization.
ComponentsRegulatory protein E2
KeywordsDNA BINDING PROTEIN / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFreire, E.
CitationJournal: Biochemistry / Year: 2007
Title: Increased Stability and DNA Site Discrimination of "Single Chain" Variants of the Dimeric beta-Barrel DNA Binding Domain of the Human Papillomavirus E2 Transcriptional Regulator.
Authors: Dellarole, M. / Sanchez, I.E. / Freire, E. / Prat-Gay, G.
History
DepositionJun 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2542
Polymers10,1581
Non-polymers961
Water72140
1
A: Regulatory protein E2
hetero molecules

A: Regulatory protein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5074
Polymers20,3152
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1840 Å2
ΔGint-31 kcal/mol
Surface area8170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.165, 43.165, 74.918
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the biological assembly is genereated by the a symmetry operation.

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Components

#1: Protein Regulatory protein E2


Mass: 10157.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 16 / Strain: HPV16 / Gene: E2 / Plasmid: PTZU18 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) plys / References: UniProt: P03120
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.21
Details: 80 mM sodium citrate, 1.53 M (NH4)2SO4, 150 mM sodium and potassium tartrate, pH 5.21, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 14, 2005
RadiationMonochromator: SI DOUBLE CRYSTAL MONOCROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→26.44 Å / Num. all: 7897 / Num. obs: 7833 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 25.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 6.8 / Num. unique all: 1103 / Rsym value: 0.185 / % possible all: 100

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Processing

Software
NameClassification
MAR345dtbdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BY9

1by9


Resolution: 1.8→26.44 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 411 -random
Rwork0.2266 ---
obs0.2273 7741 98.1 %-
all-7889 --
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms602 0 5 40 647
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005226
X-RAY DIFFRACTIONc_angle_deg1.07807

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