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- PDB-2idv: Crystal structure of wheat C113S mutant EIF4E bound TO 7-methyl-GDP -

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Basic information

Entry
Database: PDB / ID: 2idv
TitleCrystal structure of wheat C113S mutant EIF4E bound TO 7-methyl-GDP
ComponentsEukaryotic translation initiation factor 4E-1
KeywordsTRANSLATION REGULATOR / EUKARYOTIC INITIATION FACTOR 4E / EIF4E / CAP / METHYL-7-GDP
Function / homology
Function and homology information


eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translational initiation / translation initiation factor activity / defense response to virus / RNA binding / nucleus / cytoplasm
Similarity search - Function
RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / Eukaryotic translation initiation factor 4E-1
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMonzingo, A.F. / Dutt-Chaudhuri, A. / Sadow, J. / Dhaliwal, S. / Hoffman, D.W. / Robertus, J.D. / Browning, K.S.
CitationJournal: Plant Physiol. / Year: 2007
Title: The structure of eukaryotic translation initiation factor-4E from wheat reveals a novel disulfide bond.
Authors: Monzingo, A.F. / Dhaliwal, S. / Dutt-Chaudhuri, A. / Lyon, A. / Sadow, J.H. / Hoffman, D.W. / Robertus, J.D. / Browning, K.S.
History
DepositionSep 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Mar 6, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6842
Polymers20,2261
Non-polymers4581
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.651, 58.227, 39.063
Angle α, β, γ (deg.)90.000, 115.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Eukaryotic translation initiation factor 4E-1 / eIF4E-1 / eIF-4E-1 / mRNA cap-binding protein / eIF-4F 25 kDa subunit / eIF-4F p26 subunit


Mass: 20225.664 Da / Num. of mol.: 1 / Fragment: residues 39-215 / Mutation: C113S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLysS / References: UniProt: P29557
#2: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 1.85 Å3/Da / Density % sol: 33.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG4000, 0.1 M HEPES, 20 mM PHENOL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 2, 2004 / Details: BLUE MAX-FLUX CONFOCAL OPTICAL SYSTEM
RadiationMonochromator: BLUE MAX-FLUX CONFOCAL OPTICAL SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 6939 / Num. obs: 6939 / % possible obs: 96.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.218 / Net I/σ(I): 16.5
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 12.4 / Num. unique all: 642 / Χ2: 1.466 / % possible all: 88.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EJ1

1ej1


Resolution: 2.3→20 Å / FOM work R set: 0.824 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 301 4.5 %RANDOM
Rwork0.2 ---
obs-6372 96.1 %-
Solvent computationBsol: 26.841 Å2
Displacement parametersBiso mean: 19.588 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 29 101 1558
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.102
X-RAY DIFFRACTIONc_mcbond_it1.2381.5
X-RAY DIFFRACTIONc_scbond_it1.7962
X-RAY DIFFRACTIONc_mcangle_it1.9692
X-RAY DIFFRACTIONc_scangle_it2.5022.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.3-2.40.325310.278717748
2.4-2.530.343340.25727761
2.53-2.690.344390.228757796
2.69-2.90.315300.204752782
2.9-3.190.245460.227750796
3.19-3.650.308400.235788828
3.65-4.580.226390.127787826
4.58-200.219420.166793835
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5m7g.parm7g.top

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