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- PDB-1jke: D-Tyr tRNATyr deacylase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1jke
TitleD-Tyr tRNATyr deacylase from Escherichia coli
ComponentsD-Tyr-tRNATyr deacylase
KeywordsHYDROLASE / beta-alpha-barrel
Function / homology
Function and homology information


Ser(Gly)-tRNA(Ala) hydrolase activity / D-aminoacyl-tRNA deacylase 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 / response to heat / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.55 Å
AuthorsFerri-Fioni, M.L. / Schmitt, E. / Soutourina, J. / Plateau, P. / Mechulam, Y. / Blanquet, S.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A representative of a new class of tRNA-dependent hydrolases.
Authors: Ferri-Fioni, M.L. / Schmitt, E. / Soutourina, J. / Plateau, P. / Mechulam, Y. / Blanquet, S.
History
DepositionJul 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-Tyr-tRNATyr deacylase
B: D-Tyr-tRNATyr deacylase
C: D-Tyr-tRNATyr deacylase
D: D-Tyr-tRNATyr deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,64516
Polymers63,8604
Non-polymers78512
Water7,548419
1
A: D-Tyr-tRNATyr deacylase
D: D-Tyr-tRNATyr deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,45310
Polymers31,9302
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-97 kcal/mol
Surface area12470 Å2
MethodPISA
2
B: D-Tyr-tRNATyr deacylase
C: D-Tyr-tRNATyr deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1926
Polymers31,9302
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-165 kcal/mol
Surface area12690 Å2
MethodPISA
3
D: D-Tyr-tRNATyr deacylase
hetero molecules

D: D-Tyr-tRNATyr deacylase
hetero molecules

B: D-Tyr-tRNATyr deacylase
hetero molecules

B: D-Tyr-tRNATyr deacylase
hetero molecules

A: D-Tyr-tRNATyr deacylase
C: D-Tyr-tRNATyr deacylase
hetero molecules

A: D-Tyr-tRNATyr deacylase
C: D-Tyr-tRNATyr deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,29032
Polymers127,7208
Non-polymers1,57024
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation3_454x-1/2,y+1/2,z-11
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11890 Å2
ΔGint-744 kcal/mol
Surface area53850 Å2
MethodPISA
4
A: D-Tyr-tRNATyr deacylase
D: D-Tyr-tRNATyr deacylase
hetero molecules

B: D-Tyr-tRNATyr deacylase
C: D-Tyr-tRNATyr deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,64516
Polymers63,8604
Non-polymers78512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557-x+1/2,y+1/2,-z+21
Buried area8490 Å2
ΔGint-278 kcal/mol
Surface area24330 Å2
MethodPISA
5
A: D-Tyr-tRNATyr deacylase
D: D-Tyr-tRNATyr deacylase
hetero molecules

B: D-Tyr-tRNATyr deacylase
C: D-Tyr-tRNATyr deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,64516
Polymers63,8604
Non-polymers78512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area8260 Å2
ΔGint-275 kcal/mol
Surface area24560 Å2
MethodPISA
6
A: D-Tyr-tRNATyr deacylase
C: D-Tyr-tRNATyr deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3228
Polymers31,9302
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-150 kcal/mol
Surface area14920 Å2
MethodPISA
7
D: D-Tyr-tRNATyr deacylase
hetero molecules

B: D-Tyr-tRNATyr deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3228
Polymers31,9302
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area1520 Å2
ΔGint-155 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.30, 82.93, 83.51
Angle α, β, γ (deg.)90.00, 128.29, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-904-

ZN

DetailsThe asymmetric unit contains two biologically active dimers. Chains B and C form the first dimer and chains A and D form the second dimer.

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Components

#1: Protein
D-Tyr-tRNATyr deacylase / O145 / ORF_o145 / hypothetical 15.9K protein (glnA-fdhE intergenic region) / HYPOTHETICAL 15.9 KDA ...O145 / ORF_o145 / hypothetical 15.9K protein (glnA-fdhE intergenic region) / HYPOTHETICAL 15.9 KDA PROTEIN IN RBN-FDHE INTERGENIC REGION


Mass: 15965.011 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YIHZ or B3887 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101Tr / References: UniProt: P0A6M4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10% PEG 8000, 0.2 M zinc acetate, 0.1 M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP at 279K
Crystal grow
*PLUS
Temperature: 6 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 %PEG80001reservoir
20.1 Msodium cacodylate1reservoirpH6.5
30.2 Mzinc acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9474 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 2001
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9474 Å / Relative weight: 1
ReflectionResolution: 1.55→41 Å / Num. all: 91706 / Num. obs: 91706 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.067 / Net I/σ(I): 5.5
Reflection shellResolution: 1.55→1.56 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1808 / Rsym value: 0.324 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 41 Å / % possible obs: 100 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.324

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.55→500 Å / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5507 6.1 %RANDOM
Rwork0.209 ---
all0.209 91706 --
obs0.209 90612 98.8 %-
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.061 Å20 Å2-1.013 Å2
2--0.021 Å20 Å2
3---1.041 Å2
Refinement stepCycle: LAST / Resolution: 1.55→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4459 0 12 419 4890
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0046
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.55→1.56 Å
RfactorNum. reflection% reflection
Rfree0.281 108 -
Rwork0.274 --
obs-1781 100 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 6.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.281 / Rfactor Rwork: 0.274

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