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- PDB-1ueb: Crystal structure of translation elongation factor P from Thermus... -

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Basic information

Entry
Database: PDB / ID: 1ueb
TitleCrystal structure of translation elongation factor P from Thermus thermophilus HB8
Componentselongation factor P
KeywordsRNA BINDING PROTEIN / Beta barrel / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


translation elongation factor activity / cytoplasm
Similarity search - Function
Translation elongation factor P/YeiP, conserved site / Elongation factor P signature. / Translation elongation factor P/YeiP, central / Translation elongation factor P / Elongation factor P, C-terminal / Translation elongation factor P/YeiP / Elongation factor P (EF-P) OB domain / Elongation factor P, C-terminal / Elongation factor P, C-terminal / Elongation factor P (EF-P) OB domain ...Translation elongation factor P/YeiP, conserved site / Elongation factor P signature. / Translation elongation factor P/YeiP, central / Translation elongation factor P / Elongation factor P, C-terminal / Translation elongation factor P/YeiP / Elongation factor P (EF-P) OB domain / Elongation factor P, C-terminal / Elongation factor P, C-terminal / Elongation factor P (EF-P) OB domain / Translation elongation factor, KOW-like / Elongation factor P (EF-P) KOW-like domain / 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
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.65 Å
AuthorsHanawa-Suetsugu, K. / Sekine, S. / Sakai, H. / Hori-Takemoto, C. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of elongation factor P from Thermus thermophilus HB8
Authors: Hanawa-Suetsugu, K. / Sekine, S. / Sakai, H. / Hori-Takemoto, C. / Terada, T. / Unzai, S. / Tame, J.R.H. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 9, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: elongation factor P
B: elongation factor P


Theoretical massNumber of molelcules
Total (without water)40,4942
Polymers40,4942
Non-polymers00
Water7,332407
1
A: elongation factor P


Theoretical massNumber of molelcules
Total (without water)20,2471
Polymers20,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: elongation factor P


Theoretical massNumber of molelcules
Total (without water)20,2471
Polymers20,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.265, 56.035, 165.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein elongation factor P / / EF-P / TT0860


Mass: 20247.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q76G20
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.8 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: lithium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 27, 2002
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 62670 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.49 / Num. unique all: 6187 / Rsym value: 0.49 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.65→39.35 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1441463.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3160 5 %RANDOM
Rwork0.213 ---
obs0.213 62587 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4249 Å2 / ksol: 0.387419 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.12 Å20 Å20 Å2
2--9.53 Å20 Å2
3----6.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.65→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 0 407 3266
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 1.65→1.73 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.333 399 5.2 %
Rwork0.293 7244 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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