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- PDB-5wx8: Human herpesvirus 6A immediate early protein 2 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5wx8
TitleHuman herpesvirus 6A immediate early protein 2 C-terminal domain
ComponentsImmediate-early protein 2
KeywordsDNA BINDING PROTEIN / Transactivator
Function / homologyHuman herpesvirus 6 immediate early protein / Human herpesvirus 6 immediate early protein / Herpesvirus intermediate/early protein 2/3 / Herpes virus intermediate/early protein 2/3 / host cell nucleus / regulation of DNA-templated transcription / DNA binding / Immediate-early protein 2
Function and homology information
Biological speciesHuman herpesvirus 6A
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsNishimura, M. / Wang, J. / Wakata, A. / Sakamoto, K. / Mori, Y.
CitationJournal: J. Virol. / Year: 2017
Title: Crystal Structure of the DNA-Binding Domain of Human Herpesvirus 6A Immediate Early Protein 2.
Authors: Nishimura, M. / Wang, J. / Wakata, A. / Sakamoto, K. / Mori, Y.
History
DepositionJan 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immediate-early protein 2
B: Immediate-early protein 2
C: Immediate-early protein 2
D: Immediate-early protein 2


Theoretical massNumber of molelcules
Total (without water)83,3344
Polymers83,3344
Non-polymers00
Water5,368298
1
A: Immediate-early protein 2
B: Immediate-early protein 2


Theoretical massNumber of molelcules
Total (without water)41,6672
Polymers41,6672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-67 kcal/mol
Surface area15840 Å2
MethodPISA
2
C: Immediate-early protein 2
D: Immediate-early protein 2


Theoretical massNumber of molelcules
Total (without water)41,6672
Polymers41,6672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-65 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.840, 39.710, 103.730
Angle α, β, γ (deg.)90.00, 110.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Immediate-early protein 2 / IE2


Mass: 20833.508 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP RESIDUES 1324-1500)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 6A (strain Uganda-1102)
Strain: Uganda-1102 / Gene: U90/U87/U86, BCLF0 / Production host: Escherichia coli (E. coli) / References: UniProt: Q77Z83
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 24% polyethylene glycol 3350, 0.2M sodium formate, 20 mM Tris-HCl (pH 8.8), 20 mM CaCl2, 1 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97905 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2.5→42.51 Å / Num. obs: 27197 / % possible obs: 97.88 % / Redundancy: 6.3 % / Net I/σ(I): 9.47

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSOct 15, 2015data reduction
XDSOct 15, 2015data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→42.508 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 26 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2701 2001 7.36 %
Rwork0.2195 --
obs0.2233 27179 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→42.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5336 0 0 298 5634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115446
X-RAY DIFFRACTIONf_angle_d1.147340
X-RAY DIFFRACTIONf_dihedral_angle_d14.9773390
X-RAY DIFFRACTIONf_chiral_restr0.058820
X-RAY DIFFRACTIONf_plane_restr0.006928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4997-2.56220.34041410.26181789X-RAY DIFFRACTION100
2.5622-2.63140.27261460.24441848X-RAY DIFFRACTION100
2.6314-2.70890.30041460.26461783X-RAY DIFFRACTION100
2.7089-2.79630.31591440.24181819X-RAY DIFFRACTION100
2.7963-2.89620.34511450.24531802X-RAY DIFFRACTION100
2.8962-3.01210.27791480.2281849X-RAY DIFFRACTION100
3.0121-3.14920.2671360.23891823X-RAY DIFFRACTION100
3.1492-3.31510.32141490.23551826X-RAY DIFFRACTION100
3.3151-3.52270.29081430.23481805X-RAY DIFFRACTION100
3.5227-3.79460.33051090.25451381X-RAY DIFFRACTION75
3.7946-4.17610.30451400.24361760X-RAY DIFFRACTION96
4.1761-4.77970.2021490.16171865X-RAY DIFFRACTION100
4.7797-6.01920.21621520.16731862X-RAY DIFFRACTION100
6.0192-42.51440.17751530.1781966X-RAY DIFFRACTION100

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