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- PDB-2dbo: Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 2dbo
TitleCrystal structure of D-Tyr-tRNA(Tyr) deacylase from Aquifex aeolicus
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / D-amino acid / D-Tyrosine / tRNA / deacylase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Ser(Gly)-tRNA(Ala) hydrolase activity / Gly-tRNA(Ala) hydrolase activity / D-tyrosyl-tRNA(Tyr) deacylase activity / D-aminoacyl-tRNA deacylase / tRNA metabolic process / D-amino acid catabolic process / aminoacyl-tRNA editing activity / tRNA binding / cytoplasm
Similarity search - Function
D-aminoacyl-tRNA deacylase DTD / D-Tyr-tRNA(Tyr) deacylase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsIshii, T. / Shibata, R. / Bessho, Y. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Aquifex aeolicus
Authors: Ishii, T. / Shibata, R. / Bessho, Y. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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: D-tyrosyl-tRNA(Tyr) deacylase


Theoretical massNumber of molelcules
Total (without water)16,9931
Polymers16,9931
Non-polymers00
Water57632
1
A: D-tyrosyl-tRNA(Tyr) deacylase

A: D-tyrosyl-tRNA(Tyr) deacylase


Theoretical massNumber of molelcules
Total (without water)33,9852
Polymers33,9852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area3950 Å2
ΔGint-17 kcal/mol
Surface area12690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.010, 76.010, 133.754
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-161-

HOH

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Components

#1: Protein D-tyrosyl-tRNA(Tyr) deacylase


Mass: 16992.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET-11b / Production host: Escherichia coli (E. coli)
References: UniProt: O66742, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 8
Details: 0.15M sodium chloride, pH 8.0, SMALL TUBES, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→38.01 Å / Num. obs: 6373 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 46.6 Å2 / Rsym value: 0.09 / Net I/σ(I): 28.8534
Reflection shellResolution: 2.76→2.86 Å / Redundancy: 13 % / Mean I/σ(I) obs: 7.72 / Num. unique all: 611 / Rsym value: 0.368 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J7G

1j7g


Resolution: 2.76→38.01 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 111177.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.284 670 10.6 %RANDOM
Rwork0.23 ---
obs-6116 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.9913 Å2 / ksol: 0.366911 e/Å3
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.34 Å212.49 Å20 Å2
2--4.34 Å20 Å2
3----8.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.76→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 0 32 1228
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.76→2.93 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 101 10.5 %
Rwork0.296 857 -
obs--93.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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