[English] 日本語
Yorodumi
- PDB-4ats: Structure of the ORF273 protein from the Acidianus two-tailed virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ats
TitleStructure of the ORF273 protein from the Acidianus two-tailed virus
ComponentsSTRUCTURAL PROTEIN ORF273Structure
KeywordsVIRAL PROTEIN / ARCHAEAL VIRUS / EXTREMOPHILES / BICAUDAVIRUS / HYPER-THERMOSTABILITY
Function / homology: / Acidianus two-tailed virus, ORF273 protein / virion component / Structural protein ORF273
Function and homology information
Biological speciesACIDIANUS TWO-TAILED VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.85 Å
AuthorsFelisberto-Rodrigues, C. / Ortiz-Lombardia, M.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of Atv(Orf273), a New Fold for a Thermo-and Acido-Stable Protein from the Acidianus Two-Tailed Virus.
Authors: Felisberto-Rodrigues, C. / Blangy, S. / Goulet, A. / Vestergaard, G. / Cambillau, C. / Garrett, R.A. / Ortiz-Lombardia, M.
History
DepositionMay 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: STRUCTURAL PROTEIN ORF273


Theoretical massNumber of molelcules
Total (without water)34,3661
Polymers34,3661
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.013, 101.013, 52.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein STRUCTURAL PROTEIN ORF273 / Structure


Mass: 34365.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACIDIANUS TWO-TAILED VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): T7 IQ PLYSS / References: UniProt: Q3V4T6
Sequence detailsTHE PROTEIN INCLUDES AN N-TERMINAL HIS-TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.7 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN AT 5.5 MG/ML IN 20 MM HEPES (PH 7.5) AND 100 MM NACL WAS MIXED TO 5%-15% PEG 8000, 0.2 M MGCL2, 0.1 M TRIS(PH 7-8). CRYSTALS WERE OBTAINED BY THE HANGING-DROP VAPOUR-DIFFUSION METHOD

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.181
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 3.85→101.01 Å / Num. obs: 2841 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 11.02 % / Biso Wilson estimate: 63.92 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 20.57
Reflection shellResolution: 3.85→3.93 Å / Redundancy: 11.63 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 5.51 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 3.85→46.92 Å / Cor.coef. Fo:Fc: 0.8648 / Cor.coef. Fo:Fc free: 0.8404 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.95
Details: RESIDUES 47-57 WERE NOT VISIBLE IN THE MAPS. REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2926 459 16.28 %RANDOM
Rwork0.2677 ---
obs0.2719 2819 99.02 %-
Displacement parametersBiso mean: 141.21 Å2
Baniso -1Baniso -2Baniso -3
1--14.5401 Å20 Å20 Å2
2---14.5401 Å20 Å2
3---29.0803 Å2
Refine analyzeLuzzati coordinate error obs: 1.379 Å
Refinement stepCycle: LAST / Resolution: 3.85→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 0 0 1951
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092000HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.062714HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d696SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes281HARMONIC5
X-RAY DIFFRACTIONt_it2000HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion19.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion257SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2181SEMIHARMONIC4
LS refinement shellResolution: 3.85→4.3 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3212 125 16.25 %
Rwork0.2893 644 -
all0.2947 769 -
obs--99.02 %
Refinement TLS params.Method: refined / Origin x: 27.2436 Å / Origin y: 8.3855 Å / Origin z: -11.0454 Å
111213212223313233
T0.4588 Å20.124 Å20.02 Å2-0.5186 Å2-0.1562 Å2--0.6079 Å2
L0 °2-0.3493 °2-0.3693 °2-0.1047 °21.3634 °2--1.4815 °2
S0.1244 Å °0.1518 Å °-0.1146 Å °0.3834 Å °0.0702 Å °-0.5853 Å °-0.3124 Å °-0.5903 Å °-0.1946 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