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- PDB-4pbr: Crystal structure of the M. jannaschii G2 tRNA synthetase variant... -

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Basic information

Entry
Database: PDB / ID: 4pbr
TitleCrystal structure of the M. jannaschii G2 tRNA synthetase variant bound to 4-(2-bromoisobutyramido)-phenylalanine (BibaF)
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / tRNA synthetase / non-natural amino acid
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-2L7 / DI(HYDROXYETHYL)ETHER / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCooley, R.B. / Karplus, P.A. / Mehl, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0448297 United States
CitationJournal: Chembiochem / Year: 2014
Title: Gleaning Unexpected Fruits from Hard-Won Synthetases: Probing Principles of Permissivity in Non-canonical Amino Acid-tRNA Synthetases.
Authors: Cooley, R.B. / Karplus, P.A. / Mehl, R.A.
History
DepositionApr 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)36,6414
Polymers36,1141
Non-polymers5273
Water2,882160
1
A: Tyrosine--tRNA ligase
hetero molecules

A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2838
Polymers72,2282
Non-polymers1,0556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area3820 Å2
ΔGint-27 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.260, 101.260, 71.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

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Components

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


Mass: 36113.906 Da / Num. of mol.: 1 / Mutation: Y32G, L65E, F108W, Q109M, D158S, L162K
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) / Strain (production host): BL21(DE3) / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-2L7 / 4-[(2-bromo-2-methylpropanoyl)amino]-L-phenylalanine


Mass: 329.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17BrN2O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20-22% PEG 300, 5% PEG 8000, 10% glycerol and 100 mM Tris
PH range: 7.8-8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→45.3 Å / Num. obs: 29723 / % possible obs: 99.5 % / Redundancy: 15.7 % / Net I/σ(I): 9.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZP1

2zp1


Resolution: 1.9→45.3 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 1465 4.93 %Random
Rwork0.1944 ---
obs0.1967 29711 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 32 160 2677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072625
X-RAY DIFFRACTIONf_angle_d0.8363533
X-RAY DIFFRACTIONf_dihedral_angle_d16.1711038
X-RAY DIFFRACTIONf_chiral_restr0.043385
X-RAY DIFFRACTIONf_plane_restr0.006453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9680.40281480.33882713X-RAY DIFFRACTION98
1.968-2.04680.36051600.29062765X-RAY DIFFRACTION99
2.0468-2.13990.33041350.26282789X-RAY DIFFRACTION100
2.1399-2.25280.31761420.24392790X-RAY DIFFRACTION99
2.2528-2.39390.281660.22852737X-RAY DIFFRACTION99
2.3939-2.57870.26861370.22622835X-RAY DIFFRACTION100
2.5787-2.83820.2861320.22062833X-RAY DIFFRACTION100
2.8382-3.24880.25911530.20092848X-RAY DIFFRACTION100
3.2488-4.09270.21211580.16252873X-RAY DIFFRACTION100
4.0927-45.30.17871340.15773063X-RAY DIFFRACTION100
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)
11.72590.24071.26341.30630.49715.2054-0.12040.12360.16080.0198-0.0726-0.0774-0.36250.62480.1310.2092-0.0268-0.01850.23780.04430.242975.520942.9804-4.3955
24.0367-0.50431.76092.7443-0.0453.9611-0.140.078-0.07240.1930.0384-0.3033-0.01490.60420.06550.2932-0.0137-0.03470.40580.0780.272985.62937.065320.7393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:195)
2X-RAY DIFFRACTION2(chain A and resid 196:310)

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