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- PDB-5v58: Crystal structure of human prolyl-tRNA synthetase in complex with... -

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Basic information

Entry
Database: PDB / ID: 5v58
TitleCrystal structure of human prolyl-tRNA synthetase in complex with Aze-SA
ComponentsBifunctional glutamate/proline--tRNA ligase
KeywordsLIGASE / Ligase / aminoacyl-tRNA synthetase / non-proteinogenic amino acids
Function / homologyAnticodon-binding / Proline-tRNA ligase, class II, C-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / S15/NS1, RNA-binding / Aminoacyl-tRNA synthetase, class II / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Proline-tRNA ligase, class IIa, archaeal-type / Glutathione S-transferase, C-terminal / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Aminoacyl-tRNA synthetase, class I, conserved site ...Anticodon-binding / Proline-tRNA ligase, class II, C-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / S15/NS1, RNA-binding / Aminoacyl-tRNA synthetase, class II / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Proline-tRNA ligase, class IIa, archaeal-type / Glutathione S-transferase, C-terminal / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Aminoacyl-tRNA synthetase, class I, conserved site / Glutamyl/glutaminyl-tRNA synthetase / WHEP-TRS domain / Prolyl-tRNA synthetase, class II / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / Prolyl-tRNA synthetase, catalytic domain / Glutathione S-transferase, C-terminal domain superfamily / Anticodon-binding domain superfamily / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / SeMet incorporation into proteins / WHEP-TRS domain profile. / Aminoacyl-transfer RNA synthetases class-II family profile. / WHEP-TRS domain signature. / Aminoacyl-transfer RNA synthetases class-I signature. / Prolyl-tRNA synthetase, C-terminal / tRNA synthetases class I (E and Q), anti-codon binding domain / Anticodon binding domain / tRNA synthetases class I (E and Q), catalytic domain / tRNA synthetase class II core domain (G, H, P, S and T) / WHEP-TRS domain / Glutathione S-transferase, C-terminal domain / Rossmann-like alpha/beta/alpha sandwich fold / long-chain fatty acid import into cell / GAIT complex / glutamate-tRNA ligase / proline-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / glutamyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / RNA stem-loop binding / tRNA aminoacylation for protein translation / GTPase binding / cellular response to interferon-gamma / ribonucleoprotein complex / cellular response to insulin stimulus / protein-containing complex assembly / negative regulation of translation / protein homodimerization activity / zinc ion binding / membrane / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm / Bifunctional glutamate/proline--tRNA ligase
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.59 Å resolution
AuthorsZhou, H. / Song, Y. / Schimmel, P.
CitationJournal: Nat Commun / Year: 2017
Title: Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.
Authors: Song, Y. / Zhou, H. / Vo, M.N. / Shi, Y. / Nawaz, M.H. / Vargas-Rodriguez, O. / Diedrich, J.K. / Yates, J.R. / Kishi, S. / Musier-Forsyth, K. / Schimmel, P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 13, 2017 / Release: Jan 10, 2018

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional glutamate/proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5583
Polyers59,0631
Non-polymers4952
Water46826
1
A: Bifunctional glutamate/proline--tRNA ligase
hetero molecules

A: Bifunctional glutamate/proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,1176
Polyers118,1272
Non-polymers9904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area (Å2)4790
ΔGint (kcal/M)-104
Surface area (Å2)37430
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)86.766, 86.766, 108.773
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP 32 2 1

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Components

#1: Protein/peptide Bifunctional glutamate/proline--tRNA ligase / Bifunctional aminoacyl-tRNA synthetase / Cell proliferation-inducing gene 32 protein / Glutamatyl-prolyl-tRNA synthetase


Mass: 59063.453 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Production host: Escherichia coli (E. coli)
References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase
#2: Chemical ChemComp-8X1 / 5'-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine


Mass: 429.408 Da / Num. of mol.: 1 / Formula: C14H19N7O7S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Formula: H2O / Water

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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: 2.08 / Density percent sol: 40.74 %
Crystal growTemp: 293 K / Method: evaporation
Details: 9% PEG3350, 250 mM sodium nitrate, 100 mM 3-(1-pyridino)-1-propane sulfonate

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Collection date: May 5, 2012
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 2.59 Å / D resolution low: 5 Å / Number obs: 14793 / Rmerge I obs: 0.057 / Chi squared: 0.963 / NetI over sigmaI: 19 / Redundancy: 10.2 % / Percent possible obs: 96.9
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber unique allChi squaredRedundancyPercent possible all
0.3372.5902.6306520.9648.10086.500
0.2282.6302.6800.85010.60095.900
0.2132.6802.7300.90410.70096.000
0.1922.7302.7900.87310.50096.500
0.1722.7902.8500.92110.60096.700
0.1642.8502.9200.93210.50096.900
0.1282.9202.9900.94910.60097.100
0.1132.9903.0700.97210.60096.900
0.1013.0703.1601.02710.50097.300
0.0863.1603.2601.07010.60097.200
0.0763.2603.3800.98010.50097.500
0.0613.3803.5101.04410.50097.300
0.0563.5103.6700.91710.30098.400
0.0503.6703.8700.91610.20097.900
0.0463.8704.1100.91610.10097.800
0.0424.1104.4300.7519.60098.400
0.0434.4304.8700.7209.60097.400
0.0414.8705.5800.8769.90098.700
0.0415.5807.0201.11610.10098.900
0.0537.02050.0001.5039.40098.400

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HVC
Correlation coeff Fo to Fc: 0.933 / Correlation coeff Fo to Fc free: 0.91 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 11.639 / Overall SU ML: 0.257 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R Free: 0.378
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å
Displacement parametersB iso max: 107.51 Å2 / B iso mean: 59.398 Å2 / B iso min: 2 Å2 / Aniso B11: -1.33 Å2 / Aniso B12: -1.33 Å2 / Aniso B13: - Å2 / Aniso B22: -1.33 Å2 / Aniso B23: - Å2 / Aniso B33: 4.3 Å2
Least-squares processR factor R free: 0.272 / R factor R work: 0.2268 / R factor obs: 0.2291 / Highest resolution: 2.59 Å / Lowest resolution: 35.54 Å / Number reflection R free: 749 / Number reflection obs: 13977 / Percent reflection R free: 5.1 / Percent reflection obs: 96.67
Refine hist #finalHighest resolution: 2.59 Å / Lowest resolution: 35.54 Å / B iso mean ligand: 49.39 / B iso mean solvent: 50.13 / Number residues total: 476
Number of atoms included #finalProtein: 3741 / Nucleic acid: 0 / Ligand: 30 / Solvent: 26 / Total: 3797
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193868
X-RAY DIFFRACTIONr_bond_other_d0.0010.0203604
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.9595257
X-RAY DIFFRACTIONr_angle_other_deg0.6953.0008276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1605.000473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34024.023174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10815.000638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.84615.00024
X-RAY DIFFRACTIONr_chiral_restr0.0500.200583
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.020885
Refine LS shellHighest resolution: 2.588 Å / R factor R free: 0.335 / R factor R free error: 0 / R factor R work: 0.291 / Lowest resolution: 2.655 Å / Number reflection R free: 53 / Number reflection R work: 931 / Number reflection all: 984 / Total number of bins used: 20 / Percent reflection obs: 89.78

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