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- PDB-5ipx: Structure of ORF49 from KSHV -

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Basic information

Entry
Database: PDB / ID: 5ipx
TitleStructure of ORF49 from KSHV
ComponentsORF49 protein
KeywordsVIRAL PROTEIN / ORF49 / KSHV / herpesvirus / lytic replication
Function / homologyBRRF1, herpesviridae / BRRF1-like protein / ORF49 / Uncharacterized protein
Function and homology information
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsHew, K. / Nordlund, P.
CitationJournal: J. Virol. / Year: 2017
Title: Structure of the Open Reading Frame 49 Protein Encoded by Kaposi's Sarcoma-Associated Herpesvirus.
Authors: Hew, K. / Veerappan, S. / Sim, D. / Cornvik, T. / Nordlund, P. / Dahlroth, S.L.
History
DepositionMar 10, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF49 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4904
Polymers37,2021
Non-polymers2883
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.630, 142.510, 71.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

21A-525-

HOH

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Components

#1: Protein ORF49 protein


Mass: 37201.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF49 / Production host: Escherichia coli (E. coli) / References: UniProt: E5LBX2, UniProt: Q76SF9*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.15 M ammonium sulfate, 0.1 M MES, 32%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.5492 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5492 Å / Relative weight: 1
ReflectionResolution: 2.4→28.6 Å / Num. obs: 17818 / % possible obs: 100 % / Redundancy: 10.2 % / Net I/σ(I): 43.8
Reflection shellResolution: 2.4→2.49 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→28.615 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 900 5.05 %
Rwork0.2099 --
obs0.2121 17805 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→28.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 15 27 2322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062353
X-RAY DIFFRACTIONf_angle_d0.6113205
X-RAY DIFFRACTIONf_dihedral_angle_d13.4311377
X-RAY DIFFRACTIONf_chiral_restr0.039362
X-RAY DIFFRACTIONf_plane_restr0.005400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.55040.29291610.22862760X-RAY DIFFRACTION100
2.5504-2.74720.32671240.23622817X-RAY DIFFRACTION100
2.7472-3.02340.3011600.24862742X-RAY DIFFRACTION100
3.0234-3.46030.30561560.24422802X-RAY DIFFRACTION100
3.4603-4.35710.23411500.18862843X-RAY DIFFRACTION100
4.3571-28.61710.19241490.18362941X-RAY DIFFRACTION100

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