[English] 日本語
Yorodumi
- PDB-3df6: The thermo- and acido-stable ORF-99 from the archaeal virus AFV1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3df6
TitleThe thermo- and acido-stable ORF-99 from the archaeal virus AFV1
ComponentsORF99
KeywordsVIRAL PROTEIN / UNKNOWN FUNCTION / archaeal virus / extremophiles / protein fold / lipothrixviridae
Function / homologyDouble Stranded RNA Binding Domain - #300 / Sulfolobus islandicus filamentous virus, Orf14 / Protein of unknown function (DUF1374) / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein ORF99
Function and homology information
Biological speciesAcidianus Filamentous Virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsGoulet, A. / Spinelli, S. / Prangishvili, D. / van Tilbeurgh, H. / Cambillau, C. / Campanacci, V.
CitationJournal: Protein Sci. / Year: 2009
Title: The thermo- and acido-stable ORF-99 from the archaeal virus AFV1
Authors: Goulet, A. / Spinelli, S. / Blangy, S. / van Tilbeurgh, H. / Leulliot, N. / Basta, T. / Prangishvili, D. / Cambillau, C. / Campanacci, V.
History
DepositionJun 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: ORF99
B: ORF99
C: ORF99
D: ORF99
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,28810
Polymers47,0474
Non-polymers2406
Water6,630368
1
A: ORF99
C: ORF99
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6846
Polymers23,5242
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-32 kcal/mol
Surface area11330 Å2
MethodPISA
2
B: ORF99
D: ORF99
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6044
Polymers23,5242
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-31 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.112, 97.688, 103.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
ORF99 / Putative uncharacterized protein


Mass: 11761.848 Da / Num. of mol.: 4 / Mutation: L27M, I70M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus Filamentous Virus 1 / Gene: ORF99 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q70LE8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 33% MPD, 0.2M CaCl2, 0.1M Hepes, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→45 Å / Num. all: 37209 / Num. obs: 37209 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 23.58 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 25
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 7 / Num. unique all: 5344 / Rsym value: 0.399 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.184 / SU ML: 0.104 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22106 1156 3.1 %RANDOM
Rwork0.1905 ---
obs0.1915 35982 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.343 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.09 Å2
Refine analyzeLuzzati coordinate error free: 0.148 Å
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 6 368 3740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223447
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9664669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9585422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7425.855193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34615662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0021512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022648
X-RAY DIFFRACTIONr_nbd_refined0.210.21520
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22369
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2940.2368
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.232
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.060.26
X-RAY DIFFRACTIONr_mcbond_it1.1771.52089
X-RAY DIFFRACTIONr_mcangle_it1.36423288
X-RAY DIFFRACTIONr_scbond_it2.37831547
X-RAY DIFFRACTIONr_scangle_it3.5484.51364
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 75 -
Rwork0.191 2632 -
obs-2632 100 %

+
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