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- PDB-4nd6: Crystal structure of apo 3-nitro-tyrosine tRNA synthetase (5B) in... -

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Basic information

Entry
Database: PDB / ID: 4nd6
TitleCrystal structure of apo 3-nitro-tyrosine tRNA synthetase (5B) in the open form
ComponentsTyrosine-tRNA ligaseTyrosine—tRNA ligase
KeywordsLIGASE / Rossmann Fold / 3-nitro-tyrosine amino-acyl tRNA synthetase / 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
Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCooley, R.B. / Driggers, C.M. / Karplus, P.A. / Mehl, R.A.
CitationJournal: Biochemistry / Year: 2014
Title: Structural Basis of Improved Second-Generation 3-Nitro-tyrosine tRNA Synthetases.
Authors: Cooley, R.B. / Feldman, J.L. / Driggers, C.M. / Bundy, T.A. / Stokes, A.L. / Karplus, P.A. / Mehl, R.A.
History
DepositionOct 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
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

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Assembly

Deposited unit
A: Tyrosine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1662
Polymers36,0741
Non-polymers921
Water2,252125
1
A: Tyrosine-tRNA ligase
hetero molecules

A: Tyrosine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3324
Polymers72,1482
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area3280 Å2
ΔGint-35 kcal/mol
Surface area28090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.140, 101.140, 73.290
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-1002-

HOH

21A-1031-

HOH

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Components

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


Mass: 36073.844 Da / Num. of mol.: 1 / Mutation: Y32H, H70C, D158S, I159A, L162R
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: MJ0389, tyrS, tyrS MJ0389 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 22-23% PEG 300, 5% PEG 8000, 10% glycerol and 100 mM Tris pH 8.0 to 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2012 / Details: Double-crystal, Si(111) liquid N2 cooled
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→50.6 Å / Num. all: 24796 / Num. obs: 23953 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.09 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
REFMACrefinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50.57 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 1189 4.96 %Random
Rwork0.1988 ---
obs0.2013 23953 --
all-23953 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→50.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 6 125 2543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082481
X-RAY DIFFRACTIONf_angle_d1.0773332
X-RAY DIFFRACTIONf_dihedral_angle_d14.579974
X-RAY DIFFRACTIONf_chiral_restr0.075370
X-RAY DIFFRACTIONf_plane_restr0.004426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0004-2.09140.341850.30141677X-RAY DIFFRACTION
2.0914-2.20170.29081470.28362938X-RAY DIFFRACTION95
2.2017-2.33970.28341670.24712904X-RAY DIFFRACTION96
2.3397-2.52030.31971530.23992969X-RAY DIFFRACTION96
2.5203-2.77390.25241690.2242973X-RAY DIFFRACTION97
2.7739-3.17520.28441510.20933022X-RAY DIFFRACTION97
3.1752-4.00020.24961620.17143060X-RAY DIFFRACTION97
4.0002-50.58610.18911550.16323221X-RAY DIFFRACTION97
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)
12.53590.01231.66511.23461.11225.0887-0.13460.01420.0766-0.0050.01620.1037-0.3190.00850.08490.2223-0.0068-0.01510.1470.02960.270474.885145.0901-5.0092
23.4758-0.6070.82462.6452-0.47144.7955-0.1078-0.21610.05520.2943-0.0964-0.4544-0.20010.52510.19740.3601-0.0544-0.11440.33430.04690.284285.169538.136320.223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:194)
2X-RAY DIFFRACTION2(chain A and resid 195:306)

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