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- PDB-5nsf: Structure of AzuAla -

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Basic information

Entry
Database: PDB / ID: 5nsf
TitleStructure of AzuAla
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / nncA
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
Chem-96Z / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.426 Å
AuthorsMartins, B.M.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2019
Title: Site-Resolved Observation of Vibrational Energy Transfer Using a Genetically Encoded Ultrafast Heater.
Authors: Baumann, T. / Hauf, M. / Schildhauer, F. / Eberl, K.B. / Durkin, P.M. / Deniz, E. / Loffler, J.G. / Acevedo-Rocha, C.G. / Jaric, J. / Martins, B.M. / Dobbek, H. / Bredenbeck, J. / Budisa, N.
History
DepositionApr 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.title
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Tyrosine--tRNA ligase
A: Tyrosine--tRNA ligase
C: Tyrosine--tRNA ligase
D: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,84814
Polymers145,4814
Non-polymers1,36810
Water3,873215
1
B: Tyrosine--tRNA ligase
C: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3076
Polymers72,7402
Non-polymers5674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tyrosine--tRNA ligase
D: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5418
Polymers72,7402
Non-polymers8016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.140, 70.633, 77.624
Angle α, β, γ (deg.)85.70, 89.75, 83.42
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules BACD

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


Mass: 36370.164 Da / Num. of mol.: 4
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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834, tyrosine-tRNA ligase

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Non-polymers , 5 types, 225 molecules

#2: Chemical
ChemComp-96Z / (2~{S})-2-azanyl-3-(2,6-dihydroazulen-1-yl)propanoic acid


Mass: 217.264 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H15NO2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Cacl2, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.426→46.272 Å / Num. obs: 153410 / % possible obs: 93 % / Redundancy: 3.67 % / Net I/σ(I): 22.88

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1168: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U7D

1u7d


Resolution: 2.426→46.272 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.81
RfactorNum. reflection% reflection
Rfree0.2398 2088 5 %
Rwork0.1824 --
obs0.1853 41771 93.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.426→46.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9793 0 87 215 10095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310085
X-RAY DIFFRACTIONf_angle_d0.89113548
X-RAY DIFFRACTIONf_dihedral_angle_d15.246267
X-RAY DIFFRACTIONf_chiral_restr0.0451485
X-RAY DIFFRACTIONf_plane_restr0.0041736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4257-2.48210.2831340.20372560X-RAY DIFFRACTION92
2.4821-2.54420.29221440.21742740X-RAY DIFFRACTION96
2.5442-2.6130.29531420.21142682X-RAY DIFFRACTION96
2.613-2.68990.30721430.21642715X-RAY DIFFRACTION95
2.6899-2.77670.27851380.20292621X-RAY DIFFRACTION93
2.7767-2.87590.2731340.20052548X-RAY DIFFRACTION90
2.8759-2.9910.27661430.2132721X-RAY DIFFRACTION96
2.991-3.12710.281420.21832708X-RAY DIFFRACTION95
3.1271-3.2920.27861420.2062684X-RAY DIFFRACTION94
3.292-3.49810.26431330.19552530X-RAY DIFFRACTION90
3.4981-3.76810.25131390.17662645X-RAY DIFFRACTION94
3.7681-4.14710.22421430.1562715X-RAY DIFFRACTION95
4.1471-4.74670.19241330.1422533X-RAY DIFFRACTION90
4.7467-5.97830.1661430.16232708X-RAY DIFFRACTION96
5.9783-46.28060.20721350.17552573X-RAY DIFFRACTION91

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