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- PDB-3agk: Crystal structure of archaeal translation termination factor, aRF1 -

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Basic information

Entry
Database: PDB / ID: 3agk
TitleCrystal structure of archaeal translation termination factor, aRF1
ComponentsPeptide chain release factor subunit 1
KeywordsTRANSLATION
Function / homology
Function and homology information


translation release factor activity, codon specific / cytoplasm
Similarity search - Function
Peptide chain release factor aRF1 / Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / eRF1 domain 2 / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 ...Peptide chain release factor aRF1 / Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / eRF1 domain 2 / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / 50S ribosomal protein L30e-like / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptide chain release factor subunit 1
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsKobayashi, K. / Kikuno, I. / Ishitani, R. / Ito, K. / Nureki, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Omnipotent role of archaeal elongation factor 1 alpha (EF1{alpha}) in translational elongation and termination, and quality control of protein synthesis
Authors: Saito, K. / Kobayashi, K. / Wada, M. / Kikuno, I. / Takusagawa, A. / Mochizuki, M. / Uchiumi, T. / Ishitani, R. / Nureki, O. / Ito, K.
History
DepositionApr 1, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Peptide chain release factor subunit 1


Theoretical massNumber of molelcules
Total (without water)42,0061
Polymers42,0061
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.443, 80.430, 87.873
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 Peptide chain release factor subunit 1 / Translation termination factor aRF1


Mass: 42005.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus / References: UniProt: Q9YAF1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 200mM Ammonium citrate tribasic, 12% PEG MME 2000, 10mM ATP, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 9, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 27344 / Num. obs: 27344 / % possible obs: 98.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 45.03 Å2 / Rsym value: 0.052 / Net I/σ(I): 40.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1309 / Rsym value: 0.359 / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→38.558 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(I): 0.07 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1366 5.01 %Random
Rwork0.2099 ---
obs0.2125 27280 98.39 %-
all-27280 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.555 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 143.99 Å2 / Biso mean: 65.97 Å2 / Biso min: 30.25 Å2
Baniso -1Baniso -2Baniso -3
1-8.1197 Å20 Å20 Å2
2---11.4901 Å20 Å2
3---3.3704 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 0 78 2811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082778
X-RAY DIFFRACTIONf_angle_d1.1163739
X-RAY DIFFRACTIONf_chiral_restr0.074427
X-RAY DIFFRACTIONf_plane_restr0.004475
X-RAY DIFFRACTIONf_dihedral_angle_d18.4661056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1750.3991320.3322501263397
2.175-2.2620.3431360.3032563269998
2.262-2.3650.3021330.2622538267198
2.365-2.490.3161360.2472571270799
2.49-2.6460.2921350.2372573270899
2.646-2.850.3361370.2252609274699
2.85-3.1370.3061390.22226232762100
3.137-3.590.2491380.19726342772100
3.59-4.5220.2361410.17126692810100
4.522-38.5650.21390.1832633277294
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.37-1.11720.29656.0635-0.92732.28880.09630.4169-0.06570.5780.05531.219-0.0202-0.0169-0.13080.4031-0.06440.13590.36180.01970.632918.4453-2.449622.1557
24.947-0.23460.12066.04330.06422.95920.14-0.0692-0.33420.0445-0.21690.10580.04420.10920.06870.30510.04730.070.3372-0.00180.3-18.567-11.006225.5526
32.65820.0538-1.13823.0842-1.2643.46650.16670.00750.1177-0.1382-0.02260.04570.00470.2654-0.06410.45760.04560.19420.36970.00560.3872-13.867615.64587.8149
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:138A1 - 138
2X-RAY DIFFRACTION2chain A and resid 139:274A139 - 274
3X-RAY DIFFRACTION3chain A and resid 275:368A275 - 368

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