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- PDB-7ulz: Crystal Structure of Methionine-tRNA ligase / Methionyl-tRNA synt... -

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Basic information

Entry
Database: PDB / ID: 7ulz
TitleCrystal Structure of Methionine-tRNA ligase / Methionyl-tRNA synthetase (MetRS) from Pseudomonas aeruginosa PAO1
ComponentsMethionine--tRNA ligase
KeywordsLIGASE / SSGCID / Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS / Pseudomonas aeruginosa / tRNA(fMet) aminoacylation / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. ...Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
METHIONINE / Methionine--tRNA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of Methionine-tRNA ligase / Methionyl-tRNA synthetase (MetRS) from Pseudomonas aeruginosa PAO1
Authors: Abendroth, J. / DeBouver, N.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionApr 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5719
Polymers62,7491
Non-polymers8228
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.900, 167.900, 72.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS


Mass: 62749.160 Da / Num. of mol.: 1 / Fragment: PsaeA.10201.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: metG, PA3482 / Plasmid: PsaeA.10201.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HYC7, methionine-tRNA ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.75 Å3/Da / Density % sol: 74.12 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Anatrace MCSG1 screen, condition D8: 1.5M Ammonium sulfate + BisTris/HCl pH 6.5: PsaeA.10201.a.B1.PW38931 at 23mg/ml + 3mM L-Methionine + 3mM AMP. Tray 320141 d7: cryo: 20% EG + compounds: puck egi5-5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 10, 2022 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 29094 / % possible obs: 99.9 % / Redundancy: 6.261 % / Biso Wilson estimate: 44.871 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.129 / Χ2: 0.889 / Net I/σ(I): 13.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.876.3230.622.8821230.9330.677100
2.87-2.956.3020.5433.3620890.9290.59399.9
2.95-3.046.3410.4334.1420190.9540.47299.9
3.04-3.136.3420.3524.9719510.9660.384100
3.13-3.236.30.3125.5119020.9770.3499.9
3.23-3.356.3120.2267.1318450.990.24799.9
3.35-3.476.3240.189.1317860.990.196100
3.47-3.616.330.13811.1117160.9950.15199.9
3.61-3.786.2830.1213.0916430.9940.13199.9
3.78-3.966.2830.10315.4415810.9940.113100
3.96-4.176.2890.08717.615000.9970.09599.9
4.17-4.436.2640.07220.3914240.9970.079100
4.43-4.736.2790.06722.3713280.9970.07399.9
4.73-5.116.2510.0623.5512650.9980.066100
5.11-5.66.2050.07121.3311600.9960.07899.9
5.6-6.266.1560.07221.1510420.9960.07899.9
6.26-7.236.1760.06323.529380.9970.069100
7.23-8.856.0310.04430.568020.9980.048100
8.85-12.525.8260.03438.696220.9990.038100
12.52-505.2680.03636.253580.9980.0496.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1 4487refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3h99 as per Morda

3h99


Resolution: 2.8→48.47 Å / SU ML: 0.3494 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1880 6.48 %0
Rwork0.175 27136 --
obs0.1766 29016 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.79 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4073 0 44 125 4242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434262
X-RAY DIFFRACTIONf_angle_d0.65265797
X-RAY DIFFRACTIONf_chiral_restr0.0425614
X-RAY DIFFRACTIONf_plane_restr0.006752
X-RAY DIFFRACTIONf_dihedral_angle_d13.64961519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.361530.28992057X-RAY DIFFRACTION99.33
2.88-2.960.27581230.26472080X-RAY DIFFRACTION99.82
2.96-3.060.27641460.25882050X-RAY DIFFRACTION99.64
3.06-3.160.2771480.23712069X-RAY DIFFRACTION99.69
3.17-3.290.29831360.22372082X-RAY DIFFRACTION99.37
3.29-3.440.22261440.21362073X-RAY DIFFRACTION99.77
3.44-3.620.2351660.20652047X-RAY DIFFRACTION99.64
3.62-3.850.18831390.1672072X-RAY DIFFRACTION99.95
3.85-4.150.16721410.14992097X-RAY DIFFRACTION99.91
4.15-4.560.14811530.12842097X-RAY DIFFRACTION99.96
4.56-5.220.1541370.12662115X-RAY DIFFRACTION100
5.22-6.580.18551510.16012110X-RAY DIFFRACTION99.91
6.58-48.470.14631430.13862187X-RAY DIFFRACTION99.4
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)
13.55345147017-0.699041276362.214938995144.326504241150.7938971432793.610974948330.230267656333-0.806264029224-0.5789330497140.340288359005-0.0492049722875-0.173841506452-0.3866505026340.522503326515-0.1985070655250.645301772822-0.0958582220426-0.03220095367760.804104532283-0.113400903320.359347869608-77.71320.4598.158
21.02219004109-0.47780016411-0.2800465444793.268336668080.1757713799431.70158517813-0.02371990575570.08511932406520.0854652939219-0.169511305172-0.0190142901716-0.344117201234-0.1563094505440.291679432170.05363554896860.356203769648-0.00910067012662-0.01038023476860.40618924548-0.04214681525920.228538668289-79.63416.2750.802
34.376629023361.582242100325.09239906640.6242385703341.760973378075.916119448410.01278718318320.34029038081-0.0435506898425-0.0438429947920.1482620780750.0734981478363-0.5069877805380.834346415341-0.1150805201260.821536982823-0.09487167323460.0839142654740.4864124323520.01797408415010.404690977511-72.37941.25716.003
40.4986452199480.692525380251-0.5033122320941.059330453040.2987034811640.873893417460.010263590145-0.09723259074430.07927259756590.0733876088121-0.0003923624806380.013549805313-0.3912474408430.1997057112570.01464581180170.499716643508-0.00711022649001-0.03905984909570.44396310032-0.02179371055690.28729348496-83.54124.99710.328
50.896308739760.685504992657-0.02166831228491.644415017610.07134021345542.112413045310.0133585440531-0.0865781972943-0.1376032071020.106076657044-0.0514233429324-0.09577142438680.41102172620.1527426226620.02072767484590.5131828409710.08718170365830.020830661930.436495373554-0.01387687470830.288583024402-80.241-14.0287.088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 608:608 )A608
2X-RAY DIFFRACTION2( CHAIN A AND RESID 3:115 )A3 - 115
3X-RAY DIFFRACTION3( CHAIN A AND RESID 116:169 )A116 - 169
4X-RAY DIFFRACTION4( CHAIN A AND RESID 170:341 )A170 - 341
5X-RAY DIFFRACTION5( CHAIN A AND RESID 342:548 )A342 - 548

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