[English] 日本語
Yorodumi
- PDB-1g61: CRYSTAL STRUCTURE OF M.JANNASCHII EIF6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g61
TitleCRYSTAL STRUCTURE OF M.JANNASCHII EIF6
ComponentsTRANSLATION INITIATION FACTOR 6
KeywordsTRANSLATION / alpha-beta-barrel velcro closure subdomain / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


maturation of 5.8S rRNA / ribosomal large subunit binding / preribosome, large subunit precursor / translation initiation factor activity / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosome binding / cytosol
Similarity search - Function
L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor 6
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsGroft, C.M. / Beckmann, R. / Sali, A. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structures of ribosome anti-association factor IF6.
Authors: Groft, C.M. / Beckmann, R. / Sali, A. / Burley, S.K.
History
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSLATION INITIATION FACTOR 6
B: TRANSLATION INITIATION FACTOR 6


Theoretical massNumber of molelcules
Total (without water)48,9622
Polymers48,9622
Non-polymers00
Water12,683704
1
A: TRANSLATION INITIATION FACTOR 6


Theoretical massNumber of molelcules
Total (without water)24,4811
Polymers24,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRANSLATION INITIATION FACTOR 6


Theoretical massNumber of molelcules
Total (without water)24,4811
Polymers24,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.067, 46.964, 84.607
Angle α, β, γ (deg.)90.00, 98.53, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein TRANSLATION INITIATION FACTOR 6 / EIF-6


Mass: 24481.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0048 / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q60357
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 31% PEG-MME 2000, 0.200M Ammonium sulfate, 0.100M MES pH 5.6, 3mM Xylitol, 10mM glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
131 %(w/v)PEG2000 MME1reservoir
2100 mMMES1reservoirpH5.6
3200 mMammonium sulfate1reservoir
43 mMxylitol1reservoir
510 %(v/v)glycerol1reservoir
61 mMTCEP1reservoir
73.5 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.91825 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2000
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91825 Å / Relative weight: 1
ReflectionResolution: 1.3→25 Å / Num. all: 110636 / Num. obs: 110636 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 34
Reflection shellResolution: 1.3→25 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 6.6 / Num. unique all: 20604 / % possible all: 93
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 25 Å / Num. measured all: 463351
Reflection shell
*PLUS
% possible obs: 95.4 %

-
Processing

Software
NameClassification
MLPHAREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.3→25 Å / σ(F): 4 / σ(I): 0 / Stereochemistry target values: CNS defined library
Details: the following residue side chains were flagged during the last round of SHELX refinement as having parameters which disagree with the restraints: 2003, 2024, 4006, 4010, 4099
RfactorNum. reflection% reflectionSelection details
Rfree0.179 11040 -Random
Rwork0.132 ---
obs0.132 110239 94 %-
all-110239 --
Refinement stepCycle: LAST / Resolution: 1.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 0 704 4090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 1.3→25 Å /
Rfactor% reflection
Rfree0.179 -
Rwork0.132 -
obs-95 %
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 25 Å / σ(F): 4 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_deg2.1

+
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://pdbjlvh1.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