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- PDB-1j7g: Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-t... -

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Basic information

Entry
Database: PDB / ID: 1j7g
TitleStructure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / D-Tyr-tRNA(Tyr) deacylase / structural genomics / hypothetical protein / Structure 2 Function Project / S2F
Function / homology
Function and homology information


Ser(Gly)-tRNA(Ala) hydrolase activity / Gly-tRNA(Ala) deacylase activity / D-tyrosyl-tRNA(Tyr) deacylase activity / D-aminoacyl-tRNA deacylase / tRNA metabolic process / D-amino acid catabolic process / 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 speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 1.64 Å
AuthorsLim, K. / Herzberg, O. / Structure 2 Function Project (S2F)
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: A Catalytic Mechanism for D-Tyr-tRNATyr Deacylase Based on the Crystal Structure of Hemophilus influenzae HI0670
Authors: Lim, K. / Tempczyk, A. / Bonander, N. / Toedt, J. / Howard, A. / Einsenstein, E. / Herzberg, O.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Functional Characterization of the D-Tyr-tRNA(Tyr) Deacylase from Escherichia coli
Authors: Soutourina, J. / Plateau, P. / Delort, F. / Peirotes, A. / Blanquet, S.
History
DepositionMay 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: 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: D-tyrosyl-tRNA(Tyr) deacylase


Theoretical massNumber of molelcules
Total (without water)15,8791
Polymers15,8791
Non-polymers00
Water3,729207
1
A: D-tyrosyl-tRNA(Tyr) deacylase

A: D-tyrosyl-tRNA(Tyr) deacylase


Theoretical massNumber of molelcules
Total (without water)31,7582
Polymers31,7582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3310 Å2
ΔGint-9 kcal/mol
Surface area12500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.47, 55.47, 128.75
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 15879.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Species: Haemophilus influenzae / Strain: Kw20 / Gene: HI0670 / Plasmid: pET15b-HI0670 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P44814, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 277 K
Method: crystal formed during dialysis of protein (2.8mg/ml)
pH: 7.5
Details: 50 mM Tris, 0.1 mM DTT, 0.1 mM EDTA, pH 7.5, crystal formed during dialysis of protein (2.8mg/ml), temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein1drop
250 mMTris-HCl1reservoirpH7.5
30.1 mMdithiothreitol1reservoir
40.1 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. all: 25510 / Num. obs: 25510 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 12.8
Reflection shellResolution: 1.64→1.71 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.135 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 352028
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
MLPHAREphasing
DMmodel building
CNSrefinement
DMphasing
RefinementMethod to determine structure: SAS / Resolution: 1.64→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.22 1352 Random
Rwork0.194 --
all-23531 -
obs-23308 -
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 1.64→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1115 0 0 207 1322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.8
LS refinement shellResolution: 1.64→1.71 Å / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.238
Refinement
*PLUS
Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.277 / Rfactor Rwork: 0.237

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