[English] 日本語
Yorodumi
- PDB-3fhd: Crystal structure of the Shutoff and Exonuclease Protein from Kap... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more