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- PDB-1tig: TRANSLATION INITIATION FACTOR 3 C-TERMINAL DOMAIN -

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Basic information

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


ribosome disassembly / translation initiation factor activity / ribosome binding / membrane / cytosol
Similarity search - Function
Translation initiation factor 3 (IF-3), C-terminal domain / Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor 3 / Translation initiation factor 3, N-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, N-terminal domain ...Translation initiation factor 3 (IF-3), C-terminal domain / Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor 3 / Translation initiation factor 3, N-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, N-terminal domain / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor IF-3
Similarity search - Component
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.
History
DepositionAug 16, 1995Processing site: BNL
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
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSLATION INITIATION FACTOR 3


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


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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

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Components

#1: Protein TRANSLATION INITIATION FACTOR 3 / 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
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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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. ...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

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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

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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
Refine-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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 23.8

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