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- PDB-5l7p: In silico-powered specific incorporation of photocaged Dopa at mu... -

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Basic information

Entry
Database: PDB / ID: 5l7p
TitleIn silico-powered specific incorporation of photocaged Dopa at multiple protein sites
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / TyrRS
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. ...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
Chem-BUU / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHauf, M. / Richter, F. / Schneider, T. / Martins, B.M. / Baumann, T. / Durkin, P. / Dobbek, H. / Moeglich, A. / Budisa, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
Beilstein-Institut zur Foerderung der Chemischen Wissenschaften Germany
CitationJournal: Chembiochem / Year: 2017
Title: Photoactivatable Mussel-Based Underwater Adhesive Proteins by an Expanded Genetic Code.
Authors: Hauf, M. / Richter, F. / Schneider, T. / Faidt, T. / Martins, B.M. / Baumann, T. / Durkin, P. / Dobbek, H. / Jacobs, K. / Moglich, A. / Budisa, N.
History
DepositionJun 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine--tRNA ligase
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3796
Polymers72,7332
Non-polymers6464
Water6,143341
1
B: Tyrosine--tRNA ligase
hetero molecules

A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3796
Polymers72,7332
Non-polymers6464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y+1/2,-z+1/21
2
A: Tyrosine--tRNA ligase
hetero molecules

B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3796
Polymers72,7332
Non-polymers6464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area4280 Å2
ΔGint-117 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.507, 78.275, 137.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 36366.254 Da / Num. of mol.: 2
Mutation: Y32A, L65I, H70A, Q109A, D158A, I159A, L162M, A167N, A180Q, D286R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Gene: tyrS, MJ0389 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834, tyrosine-tRNA ligase

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Non-polymers , 5 types, 345 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BUU / (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid


Mass: 332.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N2O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M CaCl2 0.1 M Hepes pH 7.5 53% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→43.235 Å / Num. obs: 48252 / % possible obs: 99.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.839 / Rsym value: 0.062 / Net I/σ(I): 25.43
Reflection shellResolution: 1.9→1.95 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1168: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1du7

1du7
PDB Unreleased entry


Resolution: 1.9→43.235 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2176 1644 3.41 %
Rwork0.1783 --
obs0.1797 48182 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→43.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4855 0 42 341 5238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125005
X-RAY DIFFRACTIONf_angle_d1.1896719
X-RAY DIFFRACTIONf_dihedral_angle_d14.1733137
X-RAY DIFFRACTIONf_chiral_restr0.062742
X-RAY DIFFRACTIONf_plane_restr0.007860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95590.3081360.243839X-RAY DIFFRACTION100
1.9559-2.0190.28781330.22013798X-RAY DIFFRACTION100
2.019-2.09120.29171360.21353842X-RAY DIFFRACTION100
2.0912-2.17490.25031350.19393828X-RAY DIFFRACTION100
2.1749-2.27390.2791360.18263826X-RAY DIFFRACTION100
2.2739-2.39370.21531360.17683852X-RAY DIFFRACTION100
2.3937-2.54370.23641360.1793850X-RAY DIFFRACTION100
2.5437-2.74010.26741360.19173862X-RAY DIFFRACTION100
2.7401-3.01580.23881380.18733882X-RAY DIFFRACTION100
3.0158-3.4520.21191380.18263903X-RAY DIFFRACTION100
3.452-4.34850.18891390.15173943X-RAY DIFFRACTION100
4.3485-43.24640.17631450.17074113X-RAY DIFFRACTION100

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