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- PDB-2ohe: Structural and mutational analysis of tRNA-Intron splicing endonu... -

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Basic information

Entry
Database: PDB / ID: 2ohe
TitleStructural and mutational analysis of tRNA-Intron splicing endonuclease from Thermoplasma acidophilum DSM 1728
ComponentstRNA-splicing endonuclease
KeywordsHYDROLASE / tRNA / Intron / splicing / endonuclease
Function / homology
Function and homology information


tRNA-intron lyase / tRNA-intron lyase activity / tRNA splicing, via endonucleolytic cleavage and ligation / nucleic acid binding / lyase activity / cytoplasm
Similarity search - Function
tRNA-splicing endonuclease, linker domain / tRNA-splicing endonuclease, archaeal long subfamily / tRNA intron endonuclease, N-terminal domain superfamily / tRNA-splicing endonuclease / tRNA intron endonuclease, catalytic domain-like / tRNA intron endonuclease, catalytic C-terminal domain / tRNA intron endonuclease, catalytic domain-like superfamily / tRNA endonuclease-like domain superfamily
Similarity search - Domain/homology
tRNA-splicing endonuclease
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKim, Y.K. / Mizutani, K. / Rhee, K.H. / Lee, W.H. / Park, S.Y. / Hwang, K.Y.
CitationJournal: J.Bacteriol. / Year: 2007
Title: Structural and Mutational Analysis of tRNA Intron-Splicing Endonuclease from Thermoplasma acidophilum DSM 1728: Catalytic Mechanism of tRNA Intron-Splicing Endonucleases
Authors: Kim, Y.K. / Mizutani, K. / Rhee, K.H. / Nam, K.H. / Lee, W.H. / Lee, E.H. / Kim, E.E. / Park, S.Y. / Hwang, K.Y.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)33,3951
Polymers33,3951
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: tRNA-splicing endonuclease

A: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)66,7902
Polymers66,7902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area3450 Å2
ΔGint-15 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.906, 46.093, 58.001
Angle α, β, γ (deg.)90.00, 92.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein tRNA-splicing endonuclease / tRNA-intron splicing endonuclease / tRNA-intron endonuclease


Mass: 33394.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM 1728 / Gene: endA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 DE3 / References: UniProt: Q9HIY5, EC: 3.1.27.9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 2.4M NaCl, 0.1M Na/K phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 12, 2006 / Details: wiggler
RadiationMonochromator: wiggler / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 35520 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.066
Reflection shellResolution: 2.7→2.9 Å / Mean I/σ(I) obs: 4.44 / Num. unique all: 1887 / Rsym value: 0.29 / % possible all: 97.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→17.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 273973.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 925 4.8 %RANDOM
Rwork0.214 ---
obs0.214 19125 81.8 %-
all-23386 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.3258 Å2 / ksol: 0.385537 e/Å3
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1--13.2 Å20 Å21.22 Å2
2--14 Å20 Å2
3----0.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.7→17.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 0 116 2472
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 105 5.1 %
Rwork0.345 1959 -
obs-1887 52.6 %
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

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