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- PDB-1iz6: Crystal Structure of Translation Initiation Factor 5A from Pyroco... -

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Basic information

Entry
Database: PDB / ID: 1iz6
TitleCrystal Structure of Translation Initiation Factor 5A from Pyrococcus Horikoshii
ComponentsInitiation Factor 5A
KeywordsBIOSYNTHETIC PROTEIN / SH3-like barrel / OB fold
Function / homology
Function and homology information


positive regulation of translational termination / positive regulation of translational elongation / translation elongation factor activity / translation initiation factor activity / ribosome binding / cytoplasm
Similarity search - Function
Translation elongation factor IF5A, archaeal / Translation elongation factor, KOW-like / Elongation factor P (EF-P) KOW-like domain / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / SH3 type barrels. - #30 ...Translation elongation factor IF5A, archaeal / Translation elongation factor, KOW-like / Elongation factor P (EF-P) KOW-like domain / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / SH3 type barrels. - #30 / Nucleic acid-binding proteins / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Translation initiation factor 5A
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYao, M. / Ohsawa, A. / Kikukawa, S. / Tanaka, I. / Kimura, M.
CitationJournal: J.BIOCHEM.(TOKYO) / Year: 2003
Title: Crystal Structure of Hyperthermophilic Archaeal Initiation Factor 5A: A Homologue of Eukaryotic Initiation Factor 5A (eIF-5A)
Authors: Yao, M. / Ohsawa, A. / Kikukawa, S. / Tanaka, I. / Kimura, M.
History
DepositionSep 25, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Initiation Factor 5A
B: Initiation Factor 5A
C: Initiation Factor 5A


Theoretical massNumber of molelcules
Total (without water)45,9173
Polymers45,9173
Non-polymers00
Water5,026279
1
A: Initiation Factor 5A


Theoretical massNumber of molelcules
Total (without water)15,3061
Polymers15,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Initiation Factor 5A


Theoretical massNumber of molelcules
Total (without water)15,3061
Polymers15,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Initiation Factor 5A


Theoretical massNumber of molelcules
Total (without water)15,3061
Polymers15,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.28, 93.28, 39.43
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Initiation Factor 5A / Translation initiation factor 5A / Hypusine-containing protein


Mass: 15305.637 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1381 / Plasmid: pET-22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O50089
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, isopropanol, Hepers, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 MHEPES-NaOH1droppH7.5
310 %isopropanol1reservoir
420 %PEG40001reservoir
510 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 20, 2001
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 25949 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.074 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3842 / Rsym value: 0.317 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 100 Å / % possible obs: 100 % / Num. measured all: 148604
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BKB

1bkb


Resolution: 2→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2588 10.1 %RANDOM
Rwork0.185 ---
all0.101 25746 --
obs-25949 100 %-
Solvent computationSolvent model: throughout / Bsol: 77.45 Å2 / ksol: 0.4885 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.749 Å20.133 Å20 Å2
2--2.749 Å20 Å2
3----5.498 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.193 Å0.108 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 0 279 3434
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.628
X-RAY DIFFRACTIONc_improper_angle_d1.148
X-RAY DIFFRACTIONc_dihedral_angle_d26.76
X-RAY DIFFRACTIONc_mcbond_it3.101
X-RAY DIFFRACTIONc_mcangle_it4.026
X-RAY DIFFRACTIONc_scbond_it4.906
X-RAY DIFFRACTIONc_scangle_it6.581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs
2-2.070.27230911.70.20123292638
2.15-2.70.2742340.1892551
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Refinement
*PLUS
Num. reflection obs: 25746 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.76
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.148

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