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- PDB-4qre: Structure of Methionyl-tRNA Synthetase in complex with 1-(4-{4-[(... -

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Basic information

Entry
Database: PDB / ID: 4qre
TitleStructure of Methionyl-tRNA Synthetase in complex with 1-(4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(4,5-dimethoxy-2-methylphenoxy)pyrimidin-2-yl}piperazin-1-yl)ethanone
ComponentsMethionyl-tRNA synthetase
KeywordsLIGASE/LIGASE INHIBITOR / protein synthesis / aminoacyl-tRNA synthetase / aminoacylation / cytosol / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / HUPs / Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta ...Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / HUPs / Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3BG / ADENOSINE-5'-TRIPHOSPHATE / :
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsHilgers, M.T.
CitationJournal: to be published
Title: Discovery and SAR of a Novel Series of Pyrimidine Antibacterials Targeting Methionyl-tRNA Synthetase
Authors: Li, X. / Hilgers, M.T. / Stidham, M. / Brown-Driver, V. / Shaw, K.J. / Finn, J.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_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

Downloads & links

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Assembly

Deposited unit
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1915
Polymers63,1171
Non-polymers1,0734
Water11,079615
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.932, 75.672, 119.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methionyl-tRNA synthetase


Mass: 63117.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: metG, CH52_03385 / Production host: Escherichia coli (E. coli) / References: UniProt: W8U1H8, methionine-tRNA ligase
#2: Chemical ChemComp-3BG / 1-(4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(4,5-dimethoxy-2-methylphenoxy)pyrimidin-2-yl}piperazin-1-yl)ethanone


Mass: 517.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31N7O4
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: PEG3350, Tris pH 7.9, ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→21.5 Å / Num. all: 61657 / Num. obs: 58516 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.7-1.78194.2
1.79-1.88195.8
1.89-2.02196.1
2.03-2.18196.7
2.19-2.39197.1
2.4-2.68197.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.37 Å
Translation2.5 Å22.37 Å

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Processing

Software
NameVersionClassificationNB
MOSFLM3.2.17data reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→21.45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2422 / WRfactor Rwork: 0.1997 / FOM work R set: 0.8518 / SU B: 4.237 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1236 / SU Rfree: 0.1207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 3141 5.1 %RANDOM
Rwork0.2024 ---
obs0.2042 -94.49 %-
all-61660 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.05 Å2 / Biso mean: 24.284 Å2 / Biso min: 3.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→21.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 71 615 4906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224407
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.9755991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03324.67212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93815743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3281518
X-RAY DIFFRACTIONr_chiral_restr0.0930.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023371
X-RAY DIFFRACTIONr_nbd_refined0.220.22265
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23023
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2462
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.233
X-RAY DIFFRACTIONr_mcbond_it0.541.52681
X-RAY DIFFRACTIONr_mcangle_it0.8724207
X-RAY DIFFRACTIONr_scbond_it1.42532041
X-RAY DIFFRACTIONr_scangle_it2.0534.51784
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 228 -
Rwork0.313 3856 -
all-4084 -
obs--86.42 %
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)
11.0469-0.27710.12630.3079-0.12660.4749-0.0329-0.118-0.01090.03630.0085-0.0065-0.0287-0.03370.0244-0.00340.00760.0058-0.06820.0017-0.016812.32411.0811.974
21.12540.67931.07262.05422.2934.3047-0.02730.10090.053-0.0502-0.06130.0647-0.1314-0.1080.0886-0.02080.0147-0.0001-0.0630.012-0.00725.71613.506-9.042
32.44020.4613-1.72233.2152-2.84769.56020.00950.0602-0.24780.34720.060.16520.2651-0.6437-0.0695-0.0022-0.04550.0163-0.1051-0.0448-0.0031-8.819-1.7530.261
412.464515.83233.868737.97742.92421.42230.1425-0.0168-0.65040.4705-0.24590.78310.8264-0.14090.103400.0007-0.0003-0.0001-0.00010.0001-14.38-12.7073.358
50.9405-0.53460.17731.77820.56130.33080.06070.0105-0.17840.0938-0.21710.1330.162-0.0830.1564-0.003-0.03330.0202-0.0067-0.04640.0106-8.8511.074-5.864
67.6998-2.23225.94682.1461-2.49169.4190.33130.7663-0.5068-0.2242-0.16020.03780.53310.6985-0.1711-0.01330.07480.0049-0.1138-0.08540.009815.502-7.426-9.182
71.88740.05820.55680.16430.40851.35140.04960.0178-0.40490.001-0.05570.15760.167-0.16290.00610.0108-0.01390.0099-0.11440.00010.0331.7120.126-3.009
80.9173-0.04410.38360.27490.02740.8113-0.01030.0462-0.0751-0.0077-0.00970.01340.06760.02630.02-0.00260.00410.0029-0.0962-0.00190.00113.9974.602-0.908
93.5109-0.81840.6836.3418-1.02073.40410.0647-0.4875-0.29770.0670.05670.29440.3434-0.5545-0.1214-0.0568-0.0540.02710.00670.07280.00543.199-3.48722.745
101.1634-0.05140.64910.3368-0.19571.1345-0.0145-0.1294-0.126-0.00030.021-0.0158-0.00190.0855-0.0065-0.04850.01120.007-0.03490.0586-0.026536.067-0.72329.9
111.7790.16740.54020.7590.18953.151-0.02890.01770.1469-0.042-0.0751-0.0049-0.40570.18310.1039-0.0315-0.0465-0.0143-0.06180.0486-0.045840.56410.49927.018
121.8634-3.0762-2.539913.26170.71934.93640.00770.193-0.4064-0.1813-0.26960.704-0.0587-0.15160.2619-0.0295-0.0175-0.0162-0.0649-0.0210.02121.9353.5034.754
132.5377-1.1235-0.85536.92472.31210.8699-0.10280.0357-0.09750.06850.0090.434-0.3569-0.41560.09380.0289-0.01140.00750.0080.0640.01727.3920.26413.785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 97
2X-RAY DIFFRACTION2A98 - 117
3X-RAY DIFFRACTION3A118 - 136
4X-RAY DIFFRACTION4A137 - 161
5X-RAY DIFFRACTION5A162 - 173
6X-RAY DIFFRACTION6A174 - 192
7X-RAY DIFFRACTION7A193 - 234
8X-RAY DIFFRACTION8A235 - 302
9X-RAY DIFFRACTION9A303 - 317
10X-RAY DIFFRACTION10A318 - 475
11X-RAY DIFFRACTION11A476 - 520
12X-RAY DIFFRACTION12A601
13X-RAY DIFFRACTION13A602

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