[English] 日本語
Yorodumi
- PDB-3ile: Crystal structure of ORF157-E86A of Acidianus filamentous virus 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ile
TitleCrystal structure of ORF157-E86A of Acidianus filamentous virus 1
ComponentsPutative uncharacterized protein
KeywordsDNA BINDING PROTEIN / virus / archaea / nuclease
Function / homologyProtein of unknown function DUF3258 / Protein of unknown function DUF3258 / Immunoglobulin-like - #2930 / Immunoglobulin-like / Sandwich / Mainly Beta / NICKEL (II) ION / Uncharacterized protein ORF157
Function and homology information
Biological speciesAcidianus filamentous virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGoulet, A. / Lichiere, J. / Prangishvili, D. / van Tilbeurgh, H. / Cambillau, C. / Campanacci, V.
CitationJournal: J.Virol. / Year: 2010
Title: ORF157 from the archaeal virus Acidianus filamentous virus 1 defines a new class of nuclease
Authors: Goulet, A. / Pina, M. / Redder, P. / Prangishvili, D. / Vera, L. / Lichiere, J. / Leulliot, N. / van Tilbeurgh, H. / Ortiz-Lombardia, M. / Campanacci, V. / Cambillau, C.
History
DepositionAug 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8622
Polymers18,8041
Non-polymers591
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.876, 63.876, 85.352
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-158-

NI

-
Components

#1: Protein Putative uncharacterized protein / ORF157


Mass: 18803.574 Da / Num. of mol.: 1 / Mutation: E86A
Source method: isolated from a genetically manipulated source
Details: TEV cleavage site inserted between attB1 and the gene of interest
Source: (gene. exp.) Acidianus filamentous virus 1 / Gene: AFV1 orf157 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q70LE6
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1M LiCl2, 0.01M NiCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3.3→45 Å / Num. obs: 3286 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 74 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.2
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 5.4 / Num. unique all: 466 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3II2

3ii2


Resolution: 3.3→32 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.854 / SU B: 107.618 / SU ML: 0.728 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31281 180 5.5 %RANDOM
Rwork0.25463 ---
obs0.2582 3088 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.86 Å2
Baniso -1Baniso -2Baniso -3
1-25.44 Å2-0 Å2-0 Å2
2--25.44 Å20 Å2
3----50.88 Å2
Refinement stepCycle: LAST / Resolution: 3.3→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 0 1 0 1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221324
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9331790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9655150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67123.38268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.21215244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.548158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02998
X-RAY DIFFRACTIONr_mcbond_it0.4511.5747
X-RAY DIFFRACTIONr_mcangle_it0.86221218
X-RAY DIFFRACTIONr_scbond_it1.1523577
X-RAY DIFFRACTIONr_scangle_it2.074.5571
LS refinement shellResolution: 3.298→3.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 14 -
Rwork0.274 221 -
obs--98.33 %
Refinement TLS params.Method: refined / Origin x: -37.499 Å / Origin y: 15.1692 Å / Origin z: 5.4412 Å
111213212223313233
T0.2686 Å20.2587 Å20.0982 Å2-0.4354 Å20.2556 Å2--0.2537 Å2
L10.3725 °2-1.6938 °2-3.7017 °2-8.8064 °22.3576 °2--9.077 °2
S-1.0762 Å °-1.589 Å °-1.3592 Å °0.1783 Å °0.677 Å °0.5727 Å °0.3054 Å °0.9964 Å °0.3992 Å °

+
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://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