[English] 日本語
Yorodumi
- PDB-2j6c: crystal structure of AFV3-109, a highly conserved protein from cr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j6c
Titlecrystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses
ComponentsAFV3-109
KeywordsVIRAL PROTEIN / VIRUS / ACIDIANUS / SULFOLOBUS / CRENARCHAEA
Function / homologyUncharacterised protein PF08960, DUF1874 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesACIDIANUS FILAMENTOUS VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKeller, J. / Leulliot, N. / Cambillau, C. / Campanacci, V. / Porciero, S. / Prangishvili, D. / Cortez, D. / Quevillon-Cheruel, S. / Van Tilbeurgh, H.
CitationJournal: Virol J. / Year: 2007
Title: Crystal Structure of Afv3-109, a Highly Conserved Protein from Crenarchaeal Viruses.
Authors: Keller, J. / Leulliot, N. / Cambillau, C. / Campanacci, V. / Porciero, S. / Prangishvili, D. / Forterre, P. / Cortez, D. / Quevillon-Cheruel, S. / Van Tilbeurgh, H.
History
DepositionSep 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AFV3-109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4302
Polymers12,3371
Non-polymers921
Water3,117173
1
A: AFV3-109
hetero molecules

A: AFV3-109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8594
Polymers24,6752
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)82.770, 83.528, 33.989
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-2006-

HOH

21A-2014-

HOH

-
Components

#1: Protein AFV3-109


Mass: 12337.417 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACIDIANUS FILAMENTOUS VIRUS 1 / Strain: 3 / Plasmid: PET9 / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 45 %
Crystal growpH: 8 / Details: 25% PEG 4000, 0.1M NAAC, 0.1M TRIS-HCL PH 8.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 16423 / % possible obs: 91.2 % / Observed criterion σ(I): 1 / Redundancy: 59 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 3.9 / % possible all: 79.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→58.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.57 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1211 5.1 %RANDOM
Rwork0.185 ---
obs0.186 22711 81.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2---0.24 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.3→58.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms866 0 6 173 1045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022884
X-RAY DIFFRACTIONr_bond_other_d0.0020.02602
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9941193
X-RAY DIFFRACTIONr_angle_other_deg0.81831492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47125.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68115174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.669153
X-RAY DIFFRACTIONr_chiral_restr0.0810.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02934
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02152
X-RAY DIFFRACTIONr_nbd_refined0.2650.2174
X-RAY DIFFRACTIONr_nbd_other0.2080.2622
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2434
X-RAY DIFFRACTIONr_nbtor_other0.0870.2512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4991.5702
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7172883
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0773389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0584.5310
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.4 53
Rwork0.352 991

+
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