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- PDB-5bqk: CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF ICP27 PROTEIN FROM HSV-1 -

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Basic information

Entry
Database: PDB / ID: 5bqk
TitleCRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF ICP27 PROTEIN FROM HSV-1
ComponentsICP27
KeywordsVIRAL PROTEIN / ICP27 / HSV-1 / alpha-helical / C-terminal domain / UL54 / zinc-binding motif
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell cytoplasm / host cell nucleus / regulation of DNA-templated transcription / RNA binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Herpes viral adaptor, REF-binding domain / Herpes viral adaptor-to-host cellular mRNA binding domain / Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family
Similarity search - Domain/homology
ICP27 / mRNA export factor
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPatel, V. / Rajakannan, V. / Dahlroth, S. / Nordlund, P.
Funding support Singapore, Sweden, 2items
OrganizationGrant numberCountry
Nanyang Technological University1 Singapore
Swedish Research Council1 Sweden
CitationJournal: J.Virol. / Year: 2015
Title: Structure of the C-Terminal Domain of the Multifunctional ICP27 Protein from Herpes Simplex Virus 1.
Authors: Patel, V. / Dahlroth, S.L. / Rajakannan, V. / Ho, H.T. / Cornvik, T. / Nordlund, P.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ICP27
B: ICP27
C: ICP27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2586
Polymers90,0623
Non-polymers1963
Water5,098283
1
A: ICP27
hetero molecules

A: ICP27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1724
Polymers60,0412
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10420 Å2
ΔGint-71 kcal/mol
Surface area21390 Å2
MethodPISA
2
B: ICP27
C: ICP27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1724
Polymers60,0412
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint-70 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.983, 120.335, 79.037
Angle α, β, γ (deg.)90.000, 100.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ICP27


Mass: 30020.678 Da / Num. of mol.: 3 / Fragment: UNP residues 328-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Gene: UL54 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3TCB5, UniProt: P10238*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 4.08 Å3/Da / Density % sol: 69.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Sodium Thiocyanate, Benzamidine Hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97893 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.997→23.795 Å / Num. obs: 89418 / % possible obs: 91.48 % / Redundancy: 2.6 % / Net I/σ(I): 1.46
Reflection shellResolution: 1.997→2.068 Å / % possible all: 93.91

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
SCALAdata scaling
SOLVEphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2→23.795 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.223 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 4475 5 %RANDOM
Rwork0.217 84943 --
obs0.2185 89418 91.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.09 Å2 / Biso mean: 36.637 Å2 / Biso min: 19.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å2-0.58 Å2
2--0.3 Å20 Å2
3----1.96 Å2
Refinement stepCycle: final / Resolution: 2→23.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 3 283 6369
Biso mean--35.71 39.63 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226221
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9568455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48521.875256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9215963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0021559
X-RAY DIFFRACTIONr_chiral_restr0.1290.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214721
X-RAY DIFFRACTIONr_mcbond_it1.061.53994
X-RAY DIFFRACTIONr_mcangle_it1.79126386
X-RAY DIFFRACTIONr_scbond_it3.13132227
X-RAY DIFFRACTIONr_scangle_it4.4294.52069
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 328 -
Rwork0.298 6359 -
all-6687 -
obs--92.91 %

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