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- PDB-4kjz: Crystal Structure of Thermus Thermophilus IF2, Apo and GDP-bound ... -

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Basic information

Entry
Database: PDB / ID: 4kjz
TitleCrystal Structure of Thermus Thermophilus IF2, Apo and GDP-bound Forms (2-474)
ComponentsTranslation initiation factor IF-2
KeywordsTRANSLATION / Translation Initiation Factor/IF2 Superfamily / GTPase / GTP
Function / homology
Function and homology information


translation initiation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2720 / Arc Repressor Mutant, subunit A - #2480 / Translation initiation factor IF- 2, domain 3 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2720 / Arc Repressor Mutant, subunit A - #2480 / Translation initiation factor IF- 2, domain 3 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation factors / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Helix non-globular / Special / Small GTP-binding protein domain / Arc Repressor Mutant, subunit A / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Translation initiation factor IF-2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEiler, D.R. / Lin, J. / Steitz, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Initiation factor 2 crystal structure reveals a different domain organization from eukaryotic initiation factor 5B and mechanism among translational GTPases.
Authors: Eiler, D. / Lin, J. / Simonetti, A. / Klaholz, B.P. / Steitz, T.A.
History
DepositionMay 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 IF-2
D: Translation initiation factor IF-2
B: Translation initiation factor IF-2
C: Translation initiation factor IF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,1506
Polymers209,2634
Non-polymers8862
Water27015
1
A: Translation initiation factor IF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7592
Polymers52,3161
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Translation initiation factor IF-2


Theoretical massNumber of molelcules
Total (without water)52,3161
Polymers52,3161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Translation initiation factor IF-2


Theoretical massNumber of molelcules
Total (without water)52,3161
Polymers52,3161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Translation initiation factor IF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7592
Polymers52,3161
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.830, 177.816, 61.793
Angle α, β, γ (deg.)90.00, 89.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Translation initiation factor IF-2 / GTP-binding protein Prokaryotic Translation Initiation Factor 2


Mass: 52315.824 Da / Num. of mol.: 4 / Fragment: UNP residues 2-474 / Mutation: T17C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: infB, TTHA0699 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48515
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsP319A IS A NATURAL VARIANT.

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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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 40 mM sodium cacodylate, pH 5.4, 100 mM calcium acetate, 10 mM glycyl-glycine, 10 mM taurine, 8% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2012
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.506
11h,-k,-l20.494
ReflectionResolution: 2.8→50.01 Å / Num. all: 63086 / Num. obs: 63086 / % possible obs: 100 % / Observed criterion σ(F): 0.38 / Observed criterion σ(I): 0.38
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.8-2.91100
2.9-3.021100
3.02-3.151100
3.15-3.321100
3.32-3.531100
3.53-50.011100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B3X

4b3x


Resolution: 2.8→46.76 Å / Cor.coef. Fo:Fc: 0.846 / Cor.coef. Fo:Fc free: 0.784 / SU B: 9.77 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27564 3077 5 %RANDOM
Rwork0.2396 ---
obs0.24138 58831 97.32 %-
all-58831 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.47 Å2
Baniso -1Baniso -2Baniso -3
1-28.5 Å20 Å22.85 Å2
2---7.77 Å2-0 Å2
3----20.73 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13637 0 56 15 13708
LS refinement shellResolution: 2.799→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 144 -
Rwork0.27 3017 -
obs--67.67 %

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