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- PDB-1vbn: Escherichia coli tyrosyl-tRNA synthetase mutant complexed with Tyr-AMS -

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Basic information

Entry
Database: PDB / ID: 1vbn
TitleEscherichia coli tyrosyl-tRNA synthetase mutant complexed with Tyr-AMS
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / protein homodimerization activity / RNA binding / ATP binding / membrane / cytosol
Similarity search - Function
: / Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine--tRNA ligase SYY-like C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site ...: / Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine--tRNA ligase SYY-like C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKobayashi, T. / Sakamoto, K. / Takimura, T. / Kamata, K. / Sekine, R. / Nishimura, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
Authors: Kobayashi, T. / Sakamoto, K. / Takimura, T. / Sekine, R. / Vincent, K. / Kamata, K. / Nishimura, S. / Yokoyama, S.
History
DepositionFeb 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 28, 2016Group: Other
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-tRNA synthetase
B: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2364
Polymers71,2172
Non-polymers1,0192
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-21 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.627, 83.627, 183.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Tyrosyl-tRNA synthetase / Tyrosine--tRNA ligase / TyrRS


Mass: 35608.320 Da / Num. of mol.: 2 / Fragment: residues 5-322 / Mutation: Y37V, Q195C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P00951, UniProt: P0AGJ9*PLUS, tyrosine-tRNA ligase
#2: Chemical ChemComp-YSA / 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / TYROSYLADENYLATE


Mass: 509.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.54 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulphate, PEG 400, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2003 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 21143 / Num. obs: 20149 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 15.7
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.9 / Num. unique all: 934 / Rsym value: 0.324 / % possible all: 93.4

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UDF

1udf
PDB Unreleased entry


Resolution: 2.7→46.73 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1849062.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1982 9.9 %RANDOM
Rwork0.217 ---
obs0.217 20115 95.2 %-
all-21129 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.731 Å2 / ksol: 0.31538 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å27.25 Å20 Å2
2--2.18 Å20 Å2
3----4.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.7→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 70 115 5207
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it3.161.5
X-RAY DIFFRACTIONc_mcangle_it52
X-RAY DIFFRACTIONc_scbond_it4.982
X-RAY DIFFRACTIONc_scangle_it7.172.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 290 9.1 %
Rwork0.321 2906 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3TYRAMS.PARAMTYRAMS.TOP

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