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- PDB-1tif: TRANSLATION INITIATION FACTOR 3 N-TERMINAL DOMAIN -

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Basic information

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


translation initiation factor activity / cytoplasm
Similarity search - Function
Translation initiation factor 3 (IF-3), N-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), N-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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
TRIMETHYL LEAD ION / Translation initiation factor IF-3
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSLATION INITIATION FACTOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4384
Polymers9,1151
Non-polymers3233
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.600, 39.200, 65.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 54

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Components

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


Mass: 9114.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: T7 / Plasmid: T7 VECTOR PET13A / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / References: UniProt: P03000
#2: Chemical ChemComp-PBM / TRIMETHYL LEAD ION


Mass: 252.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9Pb
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37.08 %
Description: THE WAVELENGHT FOR DATA COLLECTION IS THE PB EDGE
Crystal grow
*PLUS
pH: 7.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.7 Mammonium sulfate1reservoir
20.1 MTris-HCl1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Apr 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionNum. obs: 6646 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.039
Reflection
*PLUS
Rmerge(I) obs: 0.039

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection
Rfree0.233 -
Rwork0.192 -
obs0.192 6646
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms788 0 6 111 905
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.32
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8

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