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- PDB-4oud: Engineered tyrosyl-tRNA synthetase with the nonstandard amino aci... -

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Basic information

Entry
Database: PDB / ID: 4oud
TitleEngineered tyrosyl-tRNA synthetase with the nonstandard amino acid L-4,4-biphenylalanine
Components(Tyrosyl-tRNA synthetase) x 2
KeywordsLIGASE / complex with L-tyrosine / Rossmann fold / tRNA
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / cytosol
Similarity search - Function
: / Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine--tRNA ligase SYY-like C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / RNA-binding S4 domain / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) ...: / Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine--tRNA ligase SYY-like C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / RNA-binding S4 domain / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TYROSINE / Tyrosine--tRNA ligase / Tyrosine--tRNA ligase / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsTakeuchi, R. / Mandell, D.J. / Lajoie, M.J. / Church, G.M. / Stoddard, B.L.
CitationJournal: Nature / Year: 2015
Title: Biocontainment of genetically modified organisms by synthetic protein design.
Authors: Mandell, D.J. / Lajoie, M.J. / Mee, M.T. / Takeuchi, R. / Kuznetsov, G. / Norville, J.E. / Gregg, C.J. / Stoddard, B.L. / Church, G.M.
History
DepositionFeb 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-tRNA synthetase
B: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1113
Polymers90,9302
Non-polymers1811
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-21 kcal/mol
Surface area35540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.340, 67.205, 90.682
Angle α, β, γ (deg.)90.00, 102.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosyl-tRNA synthetase


Mass: 47399.477 Da / Num. of mol.: 1 / Mutation: L49A, F236A, W260A, T263A, F271W, F275G, L303BIF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MC4100 / Gene: tyrS, BN896_1452 / Production host: Escherichia coli (E. coli)
References: UniProt: U6N9P2, UniProt: A0A0H2UKY9*PLUS, tyrosine-tRNA ligase
#2: Protein Tyrosyl-tRNA synthetase


Mass: 43530.457 Da / Num. of mol.: 1 / Mutation: L49A, F236A, W260A, T263A, F271W, F275G, L303BIF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MC4100 / Gene: tyrS, BN896_1452 / Production host: Escherichia coli (E. coli)
References: UniProt: U6N9P2, UniProt: A0A0H2UKZ0*PLUS, tyrosine-tRNA ligase
#3: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 355 THROUGH 402 ARE MISSING IN THE COORDINATES OF CHAIN B. HOWEVER THE AUTHORS SEE THE ...RESIDUES 355 THROUGH 402 ARE MISSING IN THE COORDINATES OF CHAIN B. HOWEVER THE AUTHORS SEE THE BACKBONE OF A 17-RESIDUE STRETCH IN THIS REGION. SINCE THEY DO NOT KNOW THE CORRESPONDENCE OF THE SEQUENCE WITH THE COORDINATES IN THIS REGION. THIS 17-RESIDUE STRETCH HAS BEEN LABELED AS UNK

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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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium malonate, 18 % PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorDetector: CCD / Date: Dec 12, 2013
RadiationMonochromator: Si 220 asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 27201 / Num. obs: 26929 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 29.2
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.65 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2YXN

2yxn


Resolution: 2.65→45 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.876 / SU B: 31.51 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 1.054 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30634 1398 5 %RANDOM
Rwork0.2218 ---
obs0.22592 26407 98.87 %-
all-26709 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.281 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å20 Å20.23 Å2
2--2.41 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.65→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6038 0 13 57 6108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196168
X-RAY DIFFRACTIONr_bond_other_d00.025868
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9558331
X-RAY DIFFRACTIONr_angle_other_deg3.616313451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7285762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78624.784301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.931151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7211535
X-RAY DIFFRACTIONr_chiral_restr0.0860.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027115
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021480
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5445.0823075
X-RAY DIFFRACTIONr_mcbond_other2.5415.0823074
X-RAY DIFFRACTIONr_mcangle_it4.2637.6063828
X-RAY DIFFRACTIONr_mcangle_other3.9625.4113829
X-RAY DIFFRACTIONr_scbond_it2.465.2953093
X-RAY DIFFRACTIONr_scbond_other2.3033.8543093
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8495.6674504
X-RAY DIFFRACTIONr_long_range_B_refined6.30928.7847311
X-RAY DIFFRACTIONr_long_range_B_other6.30128.7797308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.716 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 101 -
Rwork0.268 1899 -
obs--97.28 %
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)
10.73070.12820.30550.09840.02050.17660.0223-0.1251-0.0281-0.0517-0.0081-0.01430.0368-0.0325-0.01420.0418-0.00760.01110.0441-0.02060.054592.85137.070995.4924
20.494-0.00960.51240.0439-0.01010.66260.0340.0667-0.03790.055-0.00310.02890.03720.0103-0.03090.07760.00010.02360.0384-0.01780.042856.90216.732647.6903
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 424
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION1A601 - 636
4X-RAY DIFFRACTION2B5 - 424
5X-RAY DIFFRACTION2A637
6X-RAY DIFFRACTION2B501 - 520

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