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- PDB-7ynw: Crystal structure of O-(2-nitrobenzyl)-L-tyrosine-tRNA sythetase ... -

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Basic information

Entry
Database: PDB / ID: 7ynw
TitleCrystal structure of O-(2-nitrobenzyl)-L-tyrosine-tRNA sythetase in complex with O-(2-nitrobenzyl)-L-tyrosine
ComponentsTyrosine--tRNA ligase
KeywordsTRANSCRIPTION / nonnatural amino acid / cell-free protein synthesis / caged amino acid / o-(2-nitrobenzyl)-L-tyrosine amino-acyl tRNA synthetase
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 / 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. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Chem-J2F / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsHosaka, T. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Int J Mol Sci / Year: 2022
Title: Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography.
Authors: Hosaka, T. / Katsura, K. / Ishizuka-Katsura, Y. / Hanada, K. / Ito, K. / Tomabechi, Y. / Inoue, M. / Akasaka, R. / Takemoto, C. / Shirouzu, M.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 29, 2023Group: 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
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7264
Polymers72,0932
Non-polymers6332
Water1,45981
1
A: Tyrosine--tRNA ligase
hetero molecules

B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7264
Polymers72,0932
Non-polymers6332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area2640 Å2
ΔGint-27 kcal/mol
Surface area29350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.480, 83.480, 488.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)

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Components

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


Mass: 36046.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: tyrS, MJ0389 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-J2F / (2~{S})-2-azanyl-3-[4-[(2-nitrophenyl)methoxy]phenyl]propanoic acid


Type: L-peptide linking / Mass: 316.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG300, 3% PEG8000, 100 mM Tris-HCl (pH8.0), 10% glycerol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→41.59 Å / Num. obs: 26487 / % possible obs: 99.9 % / Redundancy: 36.042 % / Biso Wilson estimate: 113.202 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.146 / Rrim(I) all: 0.148 / Χ2: 1.161 / Net I/σ(I): 17.35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible allRmerge(I) obs
2.64-2.834.0840.1649000.79915.49799.9
2.8-2.9937.780.9445520.9434.071004.016
2.99-3.2338.3632.3643440.9751.84299.91.818
3.23-3.5437.8835.940320.9960.70199.90.691
3.54-3.9636.99113.136830.9980.31799.90.312
3.96-4.5734.94327.7832590.9990.1399.90.128
4.57-5.631.8841.2628420.9990.0911000.089
5.6-7.9236.69955.53225610.0631000.062
7.92-41.5932.21786.7914100.9990.03998.50.038

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J1U

1j1u


Resolution: 2.79→41.59 Å / SU ML: 0.5247 / Cross valid method: FREE R-VALUE / σ(F): 0.46 / Phase error: 42.0219
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2973 1678 6.48 %
Rwork0.2595 43733 -
obs0.2621 26487 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 136.8 Å2
Refinement stepCycle: LAST / Resolution: 2.79→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4912 0 46 81 5039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325038
X-RAY DIFFRACTIONf_angle_d0.58886757
X-RAY DIFFRACTIONf_chiral_restr0.0408738
X-RAY DIFFRACTIONf_plane_restr0.0048869
X-RAY DIFFRACTIONf_dihedral_angle_d25.97252001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.830.51891380.4311965X-RAY DIFFRACTION98.69
2.83-2.880.46121390.4271997X-RAY DIFFRACTION98.39
2.88-2.930.34781310.42561938X-RAY DIFFRACTION98.34
2.93-2.980.44761450.42172039X-RAY DIFFRACTION98.6
2.98-3.040.43181380.39711909X-RAY DIFFRACTION98.46
3.04-3.10.42161340.38912028X-RAY DIFFRACTION98.14
3.1-3.170.49991330.40061919X-RAY DIFFRACTION97.44
3.17-3.240.39381350.38721995X-RAY DIFFRACTION97.53
3.24-3.320.43591350.34921968X-RAY DIFFRACTION97.81
3.32-3.410.35431400.3341958X-RAY DIFFRACTION98.54
3.41-3.510.37851430.32132008X-RAY DIFFRACTION98.58
3.51-3.630.33561460.28862027X-RAY DIFFRACTION98.91
3.63-3.760.37191340.27561955X-RAY DIFFRACTION98.91
3.76-3.910.38191370.28041995X-RAY DIFFRACTION98.52
3.91-4.090.32491390.26361959X-RAY DIFFRACTION98.22
4.09-4.30.30251350.24822000X-RAY DIFFRACTION98.98
4.3-4.570.30611310.2262010X-RAY DIFFRACTION99.3
4.57-4.920.26611470.2182034X-RAY DIFFRACTION99.91
4.92-5.420.24521340.23731983X-RAY DIFFRACTION99.86
5.42-6.20.33251380.27422011X-RAY DIFFRACTION99.81
6.2-7.80.30471390.23812019X-RAY DIFFRACTION99.95
7.81-41.590.18641380.19042016X-RAY DIFFRACTION98.94
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)
17.291511632730.1435400622212.565451665385.618239801743.594003325997.22272989259-0.5447075905510.4579851751650.165908386737-1.27313654970.69626351175-0.436469337779-1.976799837-0.05327351737520.04178514100281.43601406912-0.5796756050620.07511742976631.2632561853-0.01672353977720.565795414768-20.771886326738.65618004-0.509309138916
27.16666026592-1.306890968451.322632166684.035533501351.908259626756.20621166597-0.437350896866-0.302745807942-0.0932264225101-0.5198177404680.428598184030.112718249657-0.810965208966-0.624927078233-0.04372665192151.00856275705-0.283874877942-0.06661243615210.9882269969090.06698862826930.516423593161-25.477342926137.367570042914.2146298295
31.30542164424-0.6455690760410.6136619005257.576723089172.359950976037.77750429745-0.481316674797-0.0479102196857-0.346522637052-1.637805211820.9802229316230.08156553682890.01984312928630.400712486707-0.7424075042121.84071205312-0.5867733535950.06367095962381.17284011521-0.1128077900960.780445455147-27.008916519924.8185237329-15.2934398562
47.017319149721.27513396842.204952827717.15815155174-4.795918807518.070135036490.2111866422920.140653379488-0.285409399995-0.906944328665-0.19220100180.08233235008340.9710176495330.8243915677050.02333047768571.533805459750.311453667650.02070243523380.7687342713740.001417451105280.559189810702-40.5178924507-2.0443187991731.4696555623
55.788177432020.5582077459910.04051427475283.95395337142-0.3791818337916.939502750580.3125024879930.001798878559990.368637125979-0.326311051393-0.406337745636-0.0743043058682-0.2878565246060.699063080826-0.002028567330671.196552803840.166555252080.07663531362910.9039906327280.05532312155360.546868654518-39.09891768923.066851546445.7786776364
65.22944469288-1.725695641063.150939128163.49755663369-2.350704275118.446884035010.4953505293140.3911211105790.175125870463-0.963187866495-0.2402747736430.3868285225740.391757357628-0.340903847374-0.2503297936611.424822700990.4318370230790.01907495971760.913440284162-0.02094698905420.701253531674-49.46176975219.8818181359716.8533066948
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 96 )AA1 - 961 - 96
22chain 'A' and (resid 97 through 183 )AA97 - 18397 - 183
33chain 'A' and (resid 184 through 306 )AA184 - 306184 - 306
44chain 'B' and (resid 1 through 95 )BC1 - 951 - 95
55chain 'B' and (resid 96 through 182 )BC96 - 18296 - 182
66chain 'B' and (resid 183 through 308 )BC183 - 308183 - 308

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