[English] 日本語
Yorodumi
- PDB-1tig: TRANSLATION INITIATION FACTOR 3 C-TERMINAL DOMAIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tig
TitleTRANSLATION INITIATION FACTOR 3 C-TERMINAL DOMAIN
ComponentsTRANSLATION INITIATION FACTOR 3Initiation factor
KeywordsRIBOSOME BINDING FACTOR / IF3 C-TERMINAL DOMAIN
Function / homology
Function and homology information


translation initiation factor activity / cytoplasm
Translation initiation factor 3 / Translation initiation factor 3, conserved site / Translation initiation factor 3, N-terminal / Translation initiation factor 3, C-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-3, N-terminal domain / Initiation factor 3 signature.
Translation initiation factor IF-3
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsBiou, V. / Shu, F. / Ramakrishnan, V.
Citation
Journal: EMBO J. / Year: 1995
Title: X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix.
Authors: Biou, V. / Shu, F. / Ramakrishnan, V.
#1: Journal: Biochemistry / Year: 1995
Title: Prokaryotic Translation Initiation Factor If3 is an Elongated Protein Consisting of Two Crystallizable Domains
Authors: Kycia, J.H. / Biou, V. / Shu, F. / Gerchman, S.E. / Graziano, V. / Ramakrishnan, V.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 16, 1995-
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSLATION INITIATION FACTOR 3


Theoretical massNumber of molelcules
Total (without water)10,7531
Polymers10,7531
Non-polymers00
Water72140
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)72.500, 30.200, 43.400
Angle α, β, γ (deg.)90.00, 100.11, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein/peptide TRANSLATION INITIATION FACTOR 3 / Initiation factor / IF3-C


Mass: 10752.569 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cell line: B834 / Gene: T7 / Plasmid: T7 VECTOR PET13A / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P03000
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O / Water
Nonpolymer detailsNOTE THAT SOME SOLVENT MOLECULES HAVE AN OCCUPANCY GREATER THAN 1.0. IF IT IS SIGNIFICANTLY GREATER ...NOTE THAT SOME SOLVENT MOLECULES HAVE AN OCCUPANCY GREATER THAN 1.0. IF IT IS SIGNIFICANTLY GREATER THAN 1.0 THEY COULD, IN FACT, BE OTHER IONS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.43 %
Description: THREE EXPERIMENTS WERE CONDUCTED USING MAD DATA COLLECTED AT THREE WAVELENGTHS ON TWO SELENOMETHIONINE CRYSTALS, USING INVERSE BEAM GEOMETRY: WAVELENGTH DATA REDUNDANCY MERGING R VALUE 0.9802 3.8 (2.9) 4.2 (9.0) 0.9795 3.8 (3.) 4.4 (10.9) 0.930 3.9 (3.9) 4.8 (13.6)
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
Conc.: 2.4 M / Common name: phosphate

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.00,0.9802,0.9795,0.930
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Mar 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.98021
30.97951
40.931
ReflectionNum. obs: 6402 / % possible obs: 99.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.042
Reflection
*PLUS
Rmerge(I) obs: 0.042

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 2→6 Å / σ(F): 0
RfactorNum. reflection
Rfree0.274 -
Rwork0.207 -
Obs0.207 6046
Displacement parametersBiso mean: 20.3 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 0 120 1002
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.612
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 23.8

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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