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- PDB-3d6u: Crystal structure of 4-(trifluoromethyldiazirinyl)phenylalanyl-tR... -

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Basic information

Entry
Database: PDB / ID: 3d6u
TitleCrystal structure of 4-(trifluoromethyldiazirinyl)phenylalanyl-tRNA synthetase
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / photocrosslinking Unnatural amino acid / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-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 ...Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Chem-T11 / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiu, W. / Tippmann, E. / Mack, A.V. / Schultz, P.G.
CitationJournal: ChemBioChem / Year: 2007
Title: A genetically encoded diazirine photocrosslinker in Escherichia coli
Authors: Tippmann, E. / Liu, W. / Summerer, D. / Mack, A.V. / Schultz, P.G.
History
DepositionMay 20, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionMay 27, 2008ID: 2Q1G
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4453
Polymers36,0921
Non-polymers3532
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tyrosyl-tRNA synthetase
hetero molecules

A: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8916
Polymers72,1842
Non-polymers7074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Buried area3120 Å2
ΔGint-28.3 kcal/mol
Surface area27080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.779, 102.779, 70.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 36091.980 Da / Num. of mol.: 1 / Mutation: Y32L, H70F, E107S, Q109M, D158P, I159L, L162E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: tyrS, MJ0389 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-T11 / 4-[3-(TRIFLUOROMETHYL)DIAZIRIDIN-3-YL]-L-PHENYLALANINE


Type: L-peptide linking / Mass: 275.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12F3N3O2
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5% PEG8K, 10-20% PEG300, 9% glycerol, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 18793 / Num. obs: 18786 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 5
Reflection shellResolution: 2.2→2.257 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.98 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.487 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.252 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27354 1013 5.1 %RANDOM
Rwork0.20052 ---
obs0.20408 18786 99.96 %-
all-18799 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.725 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 23 141 2618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222519
X-RAY DIFFRACTIONr_angle_refined_deg2.0482.0113385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1835305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06224.818110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.76815503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2561514
X-RAY DIFFRACTIONr_chiral_restr0.1490.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021836
X-RAY DIFFRACTIONr_nbd_refined0.2460.21328
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.211
X-RAY DIFFRACTIONr_mcbond_it1.2731.51579
X-RAY DIFFRACTIONr_mcangle_it2.06822470
X-RAY DIFFRACTIONr_scbond_it3.49831054
X-RAY DIFFRACTIONr_scangle_it5.3434.5912
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 88 -
Rwork0.221 1345 -
obs--100 %

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