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- PDB-4py2: Crystal structure of methionyl-tRNA synthetase MetRS from Brucell... -

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Basic information

Entry
Database: PDB / ID: 4py2
TitleCrystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis in complex with inhibitor 1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA
ComponentsMethionine--tRNA ligase
Keywordsligase/ligase inhibitor / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / ligase / Methionyl-tRNA synthetase / ligase-ligase inhibitor complex
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Methionine-tRNA synthetase, type 2 / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Methionyl/Leucyl tRNA synthetase ...Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Methionine-tRNA synthetase, type 2 / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-43E / Methionine--tRNA ligase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2016
Title: Brucella melitensis Methionyl-tRNA-Synthetase (MetRS), a Potential Drug Target for Brucellosis.
Authors: Ojo, K.K. / Ranade, R.M. / Zhang, Z. / Dranow, D.M. / Myers, J.B. / Choi, R. / Nakazawa Hewitt, S. / Edwards, T.E. / Davies, D.R. / Lorimer, D. / Boyle, S.M. / Barrett, L.K. / Buckner, F.S. ...Authors: Ojo, K.K. / Ranade, R.M. / Zhang, Z. / Dranow, D.M. / Myers, J.B. / Choi, R. / Nakazawa Hewitt, S. / Edwards, T.E. / Davies, D.R. / Lorimer, D. / Boyle, S.M. / Barrett, L.K. / Buckner, F.S. / Fan, E. / Van Voorhis, W.C.
History
DepositionMar 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: Methionine--tRNA ligase
B: Methionine--tRNA ligase
C: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,52313
Polymers181,0133
Non-polymers1,50910
Water9,872548
1
A: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7583
Polymers60,3381
Non-polymers4202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9446
Polymers60,3381
Non-polymers6075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8204
Polymers60,3381
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.010, 99.480, 104.000
Angle α, β, γ (deg.)110.470, 87.240, 99.990
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 3 - 508 / Label seq-ID: 24 - 529

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 60337.766 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 2308 / Gene: metG, BAB1_1014 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YQ76, methionine-tRNA ligase
#2: Chemical ChemComp-43E / 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea


Mass: 358.286 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H17Cl2N3OS
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: CSHTa10: 0.2M ammonium acetate, 0.1M sodium acetate trihydrate, pH 4.6. 30% PEG-4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.15→97.43 Å / Num. all: 90572 / Num. obs: 88924 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 38.461 Å2 / Rmerge(I) obs: 0.066 / Χ2: 0.964 / Net I/σ(I): 15.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.210.5362.7325682645097.3
2.21-2.270.4313.3625638644397.3
2.27-2.330.363.9524332611797.8
2.33-2.40.3084.6424116605997.7
2.4-2.480.255.5823530591797.9
2.48-2.570.2126.6322195558297.7
2.57-2.670.1638.4622005553998.2
2.67-2.780.13310.1620753522698.1
2.78-2.90.11311.8620057504998.2
2.9-3.040.08714.9319304486698.5
3.04-3.210.06618.7918405465798.6
3.21-3.40.05223.1317242435898.5
3.4-3.630.04128.3216082409598.9
3.63-3.930.03632.4114918380498.9
3.93-4.30.03137.0913914355199
4.3-4.810.02839.7912516319899
4.81-5.550.02938.5311012283099
5.55-6.80.03137.69151236098.9
6.8-9.620.02643.437043183999.3
9.620.02544348898497.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4LNE

4lne
PDB Unreleased entry


Resolution: 2.15→97.43 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2032 / WRfactor Rwork: 0.1686 / FOM work R set: 0.8488 / SU B: 10.191 / SU ML: 0.132 / SU R Cruickshank DPI: 0.2286 / SU Rfree: 0.1768 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 4393 4.9 %RANDOM
Rwork0.1777 ---
obs0.1794 88924 98.27 %-
all-93317 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.02 Å2 / Biso mean: 35.976 Å2 / Biso min: 15.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.48 Å2-0.38 Å2
2---0.95 Å20.27 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.15→97.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11480 0 94 548 12122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911974
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210918
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.95116317
X-RAY DIFFRACTIONr_angle_other_deg1.059324949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50251492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49923.264576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.637151744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8231592
X-RAY DIFFRACTIONr_chiral_restr0.0770.21733
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113899
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022942
X-RAY DIFFRACTIONr_mcbond_it1.4672.4725938
X-RAY DIFFRACTIONr_mcbond_other1.4672.4725937
X-RAY DIFFRACTIONr_mcangle_it2.2033.6977422
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A281370.08
12B281370.08
21A288140.07
22C288140.07
31B289040.07
32C289040.07
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 299 -
Rwork0.237 6140 -
all-6439 -
obs--97.19 %
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)
10.21080.06120.06090.42570.45030.52290.08-0.0265-0.01120.08920.0181-0.09820.0935-0.0387-0.09810.08590.0084-0.03950.0648-0.00650.178821.2849.22717.736
26.7641-1.09940.81340.9287-0.71420.58910.2758-0.1715-0.275-0.1585-0.12310.13460.06530.0421-0.15270.12470.0868-0.01710.0890.01790.205548.2771.462-4.624
30.05140.03740.1660.62530.81991.41470.0268-0.011-0.0529-0.06880.1939-0.1557-0.04280.1616-0.22070.0262-0.01730.00970.09-0.04260.204627.25616.82413.385
40.4729-0.0260.12580.74610.72730.8420.0255-0.0721-0.07230.0130.0327-0.1237-0.0006-0.059-0.05820.01080.0059-0.02530.1360.02210.158222.27536.96544.56
50.4399-0.28770.15860.5241-0.14770.528-0.064-0.0666-0.03230.00810.06570.0803-0.0415-0.0576-0.00170.0342-0.002-0.01310.122-0.00250.10679.413-32.4535.298
612.3486.7531-5.928810.9676-5.69213.69870.635-0.17481.6422-0.04320.13040.8345-0.12190.0892-0.76540.16560.05830.07480.3508-0.06870.224530.255-23.38652.38
70.4715-0.39940.32980.377-0.31760.6278-0.0232-0.0034-0.00560.0148-0.00950.0123-0.02550.05220.03270.0389-0.0033-0.010.1166-0.00920.098919.551-33.76632.482
80.1605-0.13740.47660.5805-0.22431.5060.0402-0.01360.0208-0.1412-0.1347-0.00040.0324-0.07750.09450.0990.0625-0.05940.1362-0.02740.0583.335-18.8321.605
90.8936-0.80140.31150.8928-0.03990.63780.07390.0127-0.1262-0.1669-0.03960.0365-0.0064-0.0847-0.03430.1454-0.03320.09770.0611-0.03190.1226-5.4113.96968.364
100.7257-0.26310.09760.4241-0.490.6637-0.19070.09720.00020.09580.0768-0.1083-0.1202-0.16630.1140.18810.01570.03360.0715-0.04450.0747-4.70327.45470.645
110.6968-0.83310.14361.07530.05550.68630.06790.05030.0392-0.1047-0.058-0.0613-0.03580.0006-0.00990.1481-0.04560.13370.0273-0.04420.12246.892.0969.696
120.6093-0.83790.01011.307-0.27520.66960.12270.03220.0491-0.1095-0.08790.0190.0910.1306-0.03480.13380.01370.09390.0671-0.05920.138420.42-17.89674.008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 123
2X-RAY DIFFRACTION2A124 - 160
3X-RAY DIFFRACTION3A161 - 357
4X-RAY DIFFRACTION4A358 - 508
5X-RAY DIFFRACTION5B3 - 126
6X-RAY DIFFRACTION6B127 - 162
7X-RAY DIFFRACTION7B163 - 331
8X-RAY DIFFRACTION8B332 - 510
9X-RAY DIFFRACTION9C3 - 99
10X-RAY DIFFRACTION10C100 - 233
11X-RAY DIFFRACTION11C234 - 372
12X-RAY DIFFRACTION12C373 - 508

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