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- PDB-1nhy: Crystal Structure of the GST-like Domain of Elongation Factor 1-g... -

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Basic information

Entry
Database: PDB / ID: 1nhy
TitleCrystal Structure of the GST-like Domain of Elongation Factor 1-gamma from Saccharomyces cerevisiae.
ComponentsElongation factor 1-gamma 1
KeywordsTRANSLATION / Protein synthesis / GST-like
Function / homology
Function and homology information


Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of translational termination / translational elongation / translation elongation factor activity / core promoter sequence-specific DNA binding / guanyl-nucleotide exchange factor activity / phospholipid binding / cytoplasmic stress granule / ribosome ...Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of translational termination / translational elongation / translation elongation factor activity / core promoter sequence-specific DNA binding / guanyl-nucleotide exchange factor activity / phospholipid binding / cytoplasmic stress granule / ribosome / DNA-binding transcription factor activity / calcium ion binding / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Elongation factor 1B gamma, C-terminal / Elongation factor EF1B gamma, C-terminal domain superfamily / Elongation factor 1 gamma, conserved domain / Elongation factor 1 (EF-1) gamma C-terminal domain profile. / Elongation factor 1 gamma, conserved domain / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal ...Elongation factor 1B gamma, C-terminal / Elongation factor EF1B gamma, C-terminal domain superfamily / Elongation factor 1 gamma, conserved domain / Elongation factor 1 (EF-1) gamma C-terminal domain profile. / Elongation factor 1 gamma, conserved domain / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Elongation factor 1-gamma 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsJeppesen, M.G. / Ortiz, P. / Kinzy, T.G. / Andersen, G.R. / Nyborg, J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Crystal Structure of the Glutathione S-Transferase-like Domain of Elongation Factor 1B{gamma} from Saccharomyces cerevisiae.
Authors: Jeppesen, M.G. / Ortiz, P. / Shepard, W. / Kinzy, T.G. / Nyborg, J. / Andersen, G.R.
History
DepositionDec 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor 1-gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0462
Polymers24,9501
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.520, 164.520, 164.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Elongation factor 1-gamma 1 / EF-1-gamma 1


Mass: 24950.051 Da / Num. of mol.: 1 / Fragment: residue 1-219, N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TEF3 / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P29547
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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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: 3.78 Å3/Da / Density % sol: 67.21 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Ammonium sulfate, EDTA, DTT, sodium azide, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 6 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12.36-2.4 Mammonium sulfate1reservoir
22 mMGSH1reservoir
33 mMdithiothreitol1reservoir
41 mM1reservoirNaN3
50.1 mMEDTA-NaOH1reservoirpH7.5
625 mMMES- NaOH1reservoirpH6.
725 mMHEPES-NaOH1reservoirpH7.
88.4 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: ADSC / Detector: CCD / Date: Apr 24, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→28 Å / Num. obs: 14125 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 93.74 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.049 / Net I/σ(I): 50.1
Reflection shellResolution: 3.01→3.17 Å / Redundancy: 0.109 % / Rmerge(I) obs: 0.362 / Rsym value: 0.33 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 99.6 % / Mean I/σ(I) obs: 7.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD
Starting model: None

Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2349 974 Random
Rwork0.2346 --
all0.2346 13747 -
obs0.2349 12773 -
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 5 0 1753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 3→3.05 Å /
RfactorNum. reflection
Rfree0.42 29
Rwork0.43 -
obs-405
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.42 / Rfactor Rwork: 0.432

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