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- PDB-1g7r: X-RAY STRUCTURE OF TRANSLATION INITIATION FACTOR IF2/EIF5B -

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Basic information

Entry
Database: PDB / ID: 1g7r
TitleX-RAY STRUCTURE OF TRANSLATION INITIATION FACTOR IF2/EIF5B
ComponentsTRANSLATION INITIATION FACTOR IF2/EIF5B
KeywordsTRANSLATION / translational GTPase
Function / homology
Function and homology information


translation initiation factor activity / GTPase activity / GTP binding
Similarity search - Function
Translation initiation factor IF- 2, domain 3 / Translation initiation factor aIF-2, archaea / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / 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 / Translation elongation factor EFTu-like, domain 2 ...Translation initiation factor IF- 2, domain 3 / Translation initiation factor aIF-2, archaea / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / 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 / 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. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Probable translation initiation factor IF-2
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRoll-Mecak, A. / Cao, C. / Dever, T.E. / Burley, S.K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding.
Authors: Roll-Mecak, A. / Cao, C. / Dever, T.E. / Burley, S.K.
History
DepositionNov 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSLATION INITIATION FACTOR IF2/EIF5B


Theoretical massNumber of molelcules
Total (without water)67,2311
Polymers67,2311
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.316, 54.355, 90.978
Angle α, β, γ (deg.)104.90, 101.33, 98.75
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TRANSLATION INITIATION FACTOR IF2/EIF5B


Mass: 67231.414 Da / Num. of mol.: 1 / Fragment: FULL LENGTH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: O26359
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M Cacodylate 5.8, 18% PEG4000, 0.2M Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
20.2 M1dropLiSO4
3100 mMcacodylate1reservoir
418 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2000 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.2→22 Å / Num. all: 86896 / Num. obs: 79984 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 30
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 4 % / Rmerge(I) obs: 0.15 / % possible all: 92
Reflection shell
*PLUS
% possible obs: 92 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→22 Å / Isotropic thermal model: isotropic / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: In REMARK 500, the list of covalent bonds that deviate from the dictionary value by more than 6RMSD is for residues that have poor density for atoms beyond (and including) CB atom
RfactorNum. reflection% reflectionSelection details
Rfree0.275 7401 -random
Rwork0.243 ---
all-86896 --
obs-79984 92 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.166 Å2-0.669 Å2-11.957 Å2
2--11.473 Å2-4.569 Å2
3----11.306 Å2
Refinement stepCycle: LAST / Resolution: 2.2→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 0 265 4541
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.7
LS refinement shellResolution: 2.2→2.21 Å /
RfactorNum. reflection
Rfree0.378 27
Rwork0.287 -
obs-337

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