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- PDB-3zxi: Crystal structure of human mitochondrial tyrosyl-tRNA synthetase ... -

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Basic information

Entry
Database: PDB / ID: 3zxi
TitleCrystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with a tyrosyl-adenylate analog
ComponentsTYROSYL-TRNA SYNTHETASE, MITOCHONDRIAL
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN-SUBSTRATE COMPLEX / ATP-BINDING / PROTEIN BIOSYNTHESIS
Function / homology
Function and homology information


mitochondrial tyrosyl-tRNA aminoacylation / L-tyrosine binding / tRNA aminoacylation / Mitochondrial tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / tRNA binding / nuclear body / translation / mitochondrial matrix ...mitochondrial tyrosyl-tRNA aminoacylation / L-tyrosine binding / tRNA aminoacylation / Mitochondrial tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / tRNA binding / nuclear body / translation / mitochondrial matrix / protein homodimerization activity / mitochondrion / RNA binding / ATP binding / cytosol
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-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 ...Tyrosine-tRNA ligase, bacterial-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 / RNA-binding S4 domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-TYA / Tyrosine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBonnefond, L. / Frugier, M. / Rudinger-Thirion, J. / Balg, C. / Chenevert, R. / Lorber, B. / Giege, R. / Sauter, C.
Citation
Journal: Cryst.Growth Des. / Year: 2011
Title: Exploiting Protein Engineering and Crystal Polymorphism for Successful X-Ray Structure Determination
Authors: Bonnefond, L. / Schellenberger, P. / Basquin, J. / Demangeat, G. / Ritzenthaler, C. / Chenevert, R. / Balg, C. / Frugier, M. / Rudinger-Thirion, J. / Giege, R. / Lorber, B. / Sauter, C.
#1: Journal: Structure / Year: 2007
Title: Crystal Structure of Human Mitochondrial Tyrosyl- tRNA Synthetase Reveals Common and Idiosyncratic Features.
Authors: Bonnefond, L. / Frugier, M. / Touze, E. / Lorber, B. / Florentz, C. / Giege, R. / Sauter, C. / Rudinger-Thirion, J.
History
DepositionAug 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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, MITOCHONDRIAL
B: TYROSYL-TRNA SYNTHETASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9164
Polymers79,9252
Non-polymers9912
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-27.5 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.140, 62.870, 196.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B

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Components

#1: Protein TYROSYL-TRNA SYNTHETASE, MITOCHONDRIAL / TYROSINE--TRNA LIGASE / TYRRS


Mass: 39962.371 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9Y2Z4, tyrosine-tRNA ligase
#2: Chemical ChemComp-TYA / PHOSPHORIC ACID 2-AMINO-3-(4-HYDROXY-PHENYL)-PROPYL ESTER ADENOSIN-5'YL ESTER


Mass: 495.403 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N6O8P
Sequence detailsTHE CONSTRUCT LACKS THE MITOCHONDRIAL TARGETING SEQUENCE (MTS) AND THE C-TERMINAL S4-LIKE DOMAIN.

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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 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: THE PROTEIN (20 MG/ML STOCK SOLUTION) WAS CRYSTALLIZED AT 293K BY VAPOR DIFFUSION (SITTING DROP) WITH A RESERVOIR SOLUTION CONTAINING 30% (M/V) PEG-4000, 0.1 M NA ACETATE PH 4.6, 0.2 M NH4 ...Details: THE PROTEIN (20 MG/ML STOCK SOLUTION) WAS CRYSTALLIZED AT 293K BY VAPOR DIFFUSION (SITTING DROP) WITH A RESERVOIR SOLUTION CONTAINING 30% (M/V) PEG-4000, 0.1 M NA ACETATE PH 4.6, 0.2 M NH4 ACETATE, 0.1 M TRIS-HCL PH 7.5, 1.2 M NA MALONATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 16741 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 65.46 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.2
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.46 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PID

2pid


Resolution: 2.75→29.937 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 34.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3067 859 5.1 %
Rwork0.2237 --
obs0.2277 16741 94.01 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 102.985 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-62.5793 Å20 Å20 Å2
2---26.929 Å20 Å2
3----35.6504 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 68 0 4928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085044
X-RAY DIFFRACTIONf_angle_d1.0576818
X-RAY DIFFRACTIONf_dihedral_angle_d20.4921894
X-RAY DIFFRACTIONf_chiral_restr0.071734
X-RAY DIFFRACTIONf_plane_restr0.004878
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2430X-RAY DIFFRACTIONPOSITIONAL
12B2430X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7502-2.92240.41771680.32022579X-RAY DIFFRACTION95
2.9224-3.14780.37171440.26722665X-RAY DIFFRACTION96
3.1478-3.46420.34621220.23382535X-RAY DIFFRACTION91
3.4642-3.96440.33481420.22722538X-RAY DIFFRACTION91
3.9644-4.9910.26951480.1912626X-RAY DIFFRACTION93
4.991-29.93910.26431350.21712939X-RAY DIFFRACTION98
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)
10.7035-0.00530.91140.72710.06961.5251-0.06270.21070.0399-0.51110.07690.1434-0.2790.74010.07370.50220.0292-0.04030.40520.10960.31352.0834-1.436118.8768
21.25210.09950.80670.50170.14721.63970.02740.4612-0.1017-0.6605-0.18110.011-0.41590.73080.16270.4963-0.1522-0.05380.51360.17810.45578.64624.408430.6261
31.2761-0.29650.36350.67090.51761.617-0.1630.0988-0.0979-1.08770.35610.6975-0.6520.1086-0.07270.98070.104-0.25920.63890.13340.6928-12.60062.70892.8818
41.16440.58960.87292.6786-0.48843.5338-0.02950.0021-0.09870.3073-0.0429-0.25610.61310.2952-0.02250.3587-0.1068-0.19190.24460.03250.291118.02930.231568.2099
50.49130.28751.03840.6360.35461.84130.15120.30670.1668-0.1016-0.24960.1053-0.27590.36420.13670.2992-0.0432-0.08790.42380.01350.44479.60293.888256.7587
62.02460.11180.96831.1939-0.15020.4842-1.05860.05430.2571.02080.33140.0154-0.71930.14450.37430.7573-0.2078-0.36720.75430.07170.636730.85558.597884.1413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 37:169)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 170:295)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 296:373)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 37:169)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 170:295)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 296:373)

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