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- PDB-4hpw: Crystal structure of Tyrosine-tRNA ligase mutant complexed with u... -

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Basic information

Entry
Database: PDB / ID: 4hpw
TitleCrystal structure of Tyrosine-tRNA ligase mutant complexed with unnatural amino acid 3-o-methyl-Tyrosine
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / 3-o-methyl tyrosine incorporation / tRNA
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
3-methoxy-L-tyrosine / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsYu, Y. / Zhou, Q. / Dong, J. / Li, J. / Xiaoxuan, L. / Mukherjee, A. / Ouyang, H. / Nilges, M. / Li, H. / Gao, F. ...Yu, Y. / Zhou, Q. / Dong, J. / Li, J. / Xiaoxuan, L. / Mukherjee, A. / Ouyang, H. / Nilges, M. / Li, H. / Gao, F. / Gong, W. / Lu, Y. / Wang, J.
CitationJournal: To be Published
Title: Crystal structure of Tyrosine-tRNA ligase mutant complexed with unnatural amino acid 3-o-methyl-Tyrosine
Authors: Yu, Y. / Zhou, Q. / Dong, J. / Li, J. / Xiaoxuan, L. / Mukherjee, A. / Ouyang, H. / Nilges, M. / Li, H. / Gao, F. / Gong, W. / Lu, Y. / Wang, J.
History
DepositionOct 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Structure summary
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)35,5052
Polymers35,2941
Non-polymers2111
Water1,72996
1
A: Tyrosine--tRNA ligase
hetero molecules

A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0104
Polymers70,5882
Non-polymers4222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2840 Å2
ΔGint-30 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.629, 38.830, 82.957
Angle α, β, γ (deg.)90.00, 90.75, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-580-

HOH

21A-585-

HOH

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Components

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


Mass: 35293.941 Da / Num. of mol.: 1 / Mutation: Y32E, L65S, H70G, Q109G, D158N, L162V
Source method: isolated from a genetically manipulated source
Details: restriction endonuclease cleavage sites: NdeI and XhoI
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: tyrS, MJ0389 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-3YM / 3-methoxy-L-tyrosine / 3-O-Methyldopa


Type: L-peptide linking / Mass: 211.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: protein sample (40mg/ml) in 25mM Tris-Cl PH8.0, 50mM NaCl mixed with equal volume of reservior solution containing 20-22% PEG3350, 0.2M (NH4)2SO4, 0.1M sodium citrate PH6.1-6.2, grow for 5 ...Details: protein sample (40mg/ml) in 25mM Tris-Cl PH8.0, 50mM NaCl mixed with equal volume of reservior solution containing 20-22% PEG3350, 0.2M (NH4)2SO4, 0.1M sodium citrate PH6.1-6.2, grow for 5 days, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 23101 / Num. obs: 22662 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.998→26.312 Å / SU ML: 0.5 / σ(F): 1.34 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 1149 5.1 %
Rwork0.1971 --
obs0.1999 22542 97.47 %
all-23127 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.645 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.1675 Å20 Å2-4.7759 Å2
2--5.1428 Å2-0 Å2
3---0.0247 Å2
Refinement stepCycle: LAST / Resolution: 1.998→26.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 15 96 2563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072536
X-RAY DIFFRACTIONf_angle_d1.0823419
X-RAY DIFFRACTIONf_dihedral_angle_d14.806995
X-RAY DIFFRACTIONf_chiral_restr0.071382
X-RAY DIFFRACTIONf_plane_restr0.004440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9976-2.08840.23781360.20532684X-RAY DIFFRACTION99
2.0884-2.19850.28521460.2082712X-RAY DIFFRACTION100
2.1985-2.33620.36741430.26822614X-RAY DIFFRACTION96
2.3362-2.51640.27291490.21562721X-RAY DIFFRACTION100
2.5164-2.76940.26251350.21252757X-RAY DIFFRACTION100
2.7694-3.16960.24831450.20392709X-RAY DIFFRACTION100
3.1696-3.99110.24391450.18122722X-RAY DIFFRACTION98
3.9911-26.31450.20711500.16592474X-RAY DIFFRACTION87
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)
13.0938-0.85421.33330.972-0.6661.67940.15440.181-0.1808-0.0875-0.13120.09840.10110.0670.00390.15480.03370.01230.1232-0.02990.114415.1981-3.823324.9736
22.2871-0.141.77450.61940.05171.4155-0.05980.06150.08930.0341-0.09440.0748-0.07870.04970.10870.16470.02660.030.18490.0060.161216.95612.351525.7888
33.7015-0.24870.28291.6072-0.51372.9027-0.03210.24830.1573-0.21990.07170.3486-0.0056-0.2036-0.04480.1443-0.0043-0.05560.1248-0.02910.2543-8.4985.426613.4813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:144)
2X-RAY DIFFRACTION2chain 'A' and (resseq 145:211)
3X-RAY DIFFRACTION3chain 'A' and (resseq 212:310)

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