[English] 日本語
Yorodumi
- PDB-3fbz: Crystal structure of ORF140 of the archaeal virus Acidianus Filam... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fbz
TitleCrystal structure of ORF140 of the archaeal virus Acidianus Filamentous Virus 1 (AFV1)
ComponentsPutative uncharacterized protein
KeywordsSTRUCTURAL PROTEIN / archaeal virus / extremophiles / lipothrixviridae
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #800 / Filamentous archaeal viruses coat protein / helical viral capsid / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / DNA binding / Mainly Alpha / Major capsid protein 1
Function and homology information
Biological speciesAcidianus Filamentous Virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsGoulet, A. / Prangishvili, D. / van Tilbeurgh, H. / Campanacci, V. / Cambillau, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage.
Authors: Goulet, A. / Blangy, S. / Redder, P. / Prangishvili, D. / Felisberto-Rodrigues, C. / Forterre, P. / Campanacci, V. / Cambillau, C.
History
DepositionNov 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,19514
Polymers63,7854
Non-polymers2,41010
Water4,378243
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2392
Polymers15,9461
Non-polymers2921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8595
Polymers15,9461
Non-polymers9134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8234
Polymers15,9461
Non-polymers8773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2743
Polymers15,9461
Non-polymers3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19150 Å2
ΔGint-58 kcal/mol
Surface area21350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.158, 81.150, 119.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Putative uncharacterized protein / ORF140


Mass: 15946.292 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus Filamentous Virus 1 / Gene: AFV1_ORF140 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q70LC6
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 17% PEG 550 MME, 0.1M Sodium Cacodylate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 25779 / % possible obs: 99.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 14.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3569 / Rsym value: 0.36 / % possible all: 96

-
Processing

Software
NameVersionClassification
SHELXSphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / SU B: 13.325 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25475 1047 4.1 %RANDOM
Rwork0.18539 ---
obs0.1882 24567 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.815 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 162 243 4397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224244
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9915773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.985511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24725.979189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50515727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5921511
X-RAY DIFFRACTIONr_chiral_restr0.10.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023063
X-RAY DIFFRACTIONr_nbd_refined0.2060.22109
X-RAY DIFFRACTIONr_nbtor_refined0.30.22945
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.2238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.223
X-RAY DIFFRACTIONr_mcbond_it0.6311.52548
X-RAY DIFFRACTIONr_mcangle_it1.01924052
X-RAY DIFFRACTIONr_scbond_it1.85331958
X-RAY DIFFRACTIONr_scangle_it2.8284.51709
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 76 -
Rwork0.207 1651 -
obs-1651 93.71 %

+
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