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- PDB-5n5u: Structure of p-boronophenylalanyl tRNA synthetase in complex with... -

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Basic information

Entry
Database: PDB / ID: 5n5u
TitleStructure of p-boronophenylalanyl tRNA synthetase in complex with p-boronophenylalanine and adenosine monophosphate
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / aminoacylation / non-natural amino acid / synthetic biology
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
4-Borono-L-phenylalanine / ADENOSINE MONOPHOSPHATE / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchiefner, A. / Skerra, A.
CitationJournal: Biochemistry / Year: 2018
Title: Structural Basis for the Specific Cotranslational Incorporation of p-Boronophenylalanine into Biosynthetic Proteins.
Authors: Schiefner, A. / Nastle, L. / Landgraf, M. / Reichert, A.J. / Skerra, A.
History
DepositionFeb 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6396
Polymers35,9771
Non-polymers6635
Water3,981221
1
A: Tyrosine--tRNA ligase
hetero molecules

A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,27912
Polymers71,9532
Non-polymers1,32510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area5210 Å2
ΔGint-110 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.582, 38.735, 82.034
Angle α, β, γ (deg.)90.000, 90.280, 90.000
Int Tables number3
Space group name H-MP121

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Components

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


Mass: 35976.734 Da / Num. of mol.: 1 / Mutation: M6L, Y32S, L65A, H70M, D158S, L162E
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)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: tyrS, MJ0389 / Plasmid: pASK75-BpaRS-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-7N8 / 4-Borono-L-phenylalanine


Type: L-peptide linking / Mass: 209.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12BNO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 % (w/v) PEG 1000, 0.2 M MgCl2, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2016
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8943 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 43906 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.43 % / Biso Wilson estimate: 31.967 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.046 / Χ2: 1.007 / Net I/σ(I): 24.36 / Num. measured all: 326242 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.77.4970.7173.1872140.9090.77199.5
1.7-1.87.5280.4135.3657120.9660.44499.6
1.8-27.5480.19110.5683160.9920.20599.8
2-37.4670.0532.33158520.9990.05499.9
3-47.1260.02958.7839100.9990.03299.9
4-67.0990.02664.5520420.9990.02899.9
6-86.9790.02564.015140.9990.027100
8-106.440.02163.051750.9990.02395.6
10-305.5440.021581710.9990.02380.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NDA

4nda


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.119 / SU ML: 0.07 / SU R Cruickshank DPI: 0.0864 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.089
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 2100 4.8 %RANDOM
Rwork0.176 ---
obs0.1777 41806 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 116.05 Å2 / Biso mean: 33.232 Å2 / Biso min: 17 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-0 Å2-1.16 Å2
2--1.97 Å20 Å2
3----0.86 Å2
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 41 222 2736
Biso mean--28.25 39.18 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192609
X-RAY DIFFRACTIONr_bond_other_d0.0020.022592
X-RAY DIFFRACTIONr_angle_refined_deg2.05123512
X-RAY DIFFRACTIONr_angle_other_deg1.05536003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8925320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28324.741116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2315521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3691516
X-RAY DIFFRACTIONr_chiral_restr0.1310.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022883
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02546
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 161 -
Rwork0.274 3035 -
all-3196 -
obs--99.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.44390.78391.70071.72380.38481.55410.198-0.1292-0.26540.0741-0.1016-0.11490.2573-0.054-0.09640.0515-0.0112-0.01660.01360.02230.040612.44724.3609100.9138
22.2968-0.75972.29670.9744-0.75675.4873-0.0389-0.02690.24350.0094-0.0607-0.0686-0.41730.01830.09960.0455-0.0040.01260.0165-0.01090.03523.119734.122491.497
35.3890.30531.32620.04060.09580.3705-0.06070.29620.1097-0.03270.0138-0.0095-0.04910.03220.0470.04340.00830.00670.0753-0.02090.04819.265334.1227100.0028
43.65050.06-0.01953.63581.22653.1866-0.0673-0.41210.11690.23940.0132-0.3875-0.16330.37810.05410.0822-0.0196-0.04130.09620.00970.058234.441938.0979111.8301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 116
2X-RAY DIFFRACTION2A117 - 178
3X-RAY DIFFRACTION3A179 - 225
4X-RAY DIFFRACTION4A226 - 309

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