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- PDB-3fhd: Crystal structure of the Shutoff and Exonuclease Protein from Kap... -

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Basic information

Entry
Database: PDB / ID: 3fhd
TitleCrystal structure of the Shutoff and Exonuclease Protein from Kaposis Sarcoma Associated Herpesvirus
ComponentsORF 37
KeywordsHYDROLASE / ENase like PD-(D/E)XK Superfamily
Function / homology
Function and homology information


exonuclease activity / endonuclease activity / host cell cytoplasm / host cell nucleus / DNA binding / metal ion binding
Similarity search - Function
Herpesvirus alkaline exonuclease, N-terminal domain / Alphaherpesvirus alkaline exonuclease / Viral alkaline exonuclease / Viral alkaline exonuclease / Restriction endonuclease type II-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman herpesvirus 8 type M
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsDahlroth, S.L. / Gurmu, D. / Schmitzberger, F. / Haas, J. / Erlandsen, H. / Nordlund, P.
CitationJournal: Febs J. / Year: 2009
Title: Crystal structure of the shutoff and exonuclease protein from the oncogenic Kaposi's sarcoma-associated herpesvirus
Authors: Dahlroth, S.L. / Gurmu, D. / Schmitzberger, F. / Engman, H. / Haas, J. / Erlandsen, H. / Nordlund, P.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: ORF 37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9375
Polymers57,6251
Non-polymers3124
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.247, 48.905, 67.294
Angle α, β, γ (deg.)95.48, 106.86, 104.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ORF 37 / Shutoff and Exonuclease Protein


Mass: 57624.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 type M / Gene: orf37 / Plasmid: pTH27 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P88925
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Lithium sulfate, 0.1M Bis-TRIS, 25%PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.210.97954
SYNCHROTRONESRF ID14-220.933
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJun 7, 2007
ADSC QUANTUM 42CCDJun 28, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystalSINGLE WAVELENGTHMx-ray1
2Diamond (111), Ge(220)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979541
20.9331
ReflectionResolution: 1.85→46.63 Å / Num. obs: 41764 / Redundancy: 3.4 % / Biso Wilson estimate: 28.119 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→46.63 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.145 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22807 2096 5.1 %RANDOM
Rwork0.18356 ---
obs0.18582 39306 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.126 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.44 Å20.29 Å2
2--0.3 Å20.27 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3591 0 16 216 3823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223697
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9515021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.725453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49823.515165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49615588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.421519
X-RAY DIFFRACTIONr_chiral_restr0.0960.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022813
X-RAY DIFFRACTIONr_nbd_refined0.1990.21555
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2200
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.211
X-RAY DIFFRACTIONr_mcbond_it0.8761.52343
X-RAY DIFFRACTIONr_mcangle_it1.48223657
X-RAY DIFFRACTIONr_scbond_it2.2731575
X-RAY DIFFRACTIONr_scangle_it3.3084.51364
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 173 -
Rwork0.287 2884 -
obs--95.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9479-0.3911-0.3042.00970.22651.4242-0.0365-0.1640.20380.21430.068-0.1234-0.249-0.0386-0.03150.0471-0.0064-0.03010.00340.00020.050912.836544.35373.4134
20.8467-0.3343-0.58941.3076-0.81722.26910.00550.2757-0.1589-0.3686-0.125-0.00280.339-0.21770.11950.0714-0.0378-0.00450.082-0.04160.06812.809329.906544.9253
31.2893-0.1537-0.28771.5794-0.2192.6063-0.053-0.0819-0.13880.0573-0.0225-0.13010.3123-0.06780.0755-0.02-0.01580.00610.0410.00540.12416.462730.379863.1555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 182
2X-RAY DIFFRACTION2A183 - 424
3X-RAY DIFFRACTION3A425 - 481

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