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- PDB-5k0t: Crystal structure of methionyl-tRNA synthetase MetRS from Brucell... -

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Basic information

Entry
Database: PDB / ID: 5k0t
TitleCrystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis in complex with inhibitor Chem 1415
ComponentsMethionine--tRNA ligase
KeywordsLIGASE / SSGCID / MetRS / methionyl-tRNA synthetase / Brucella melitensis / protein biosynthesis / 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 / 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-415 / Methionine--tRNA ligase
Similarity search - Component
Biological speciesBrucella suis biovar 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsSeattle 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
DepositionMay 17, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionMay 25, 2016ID: 4PPW
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 27, 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 / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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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)182,55314
Polymers181,0133
Non-polymers1,54011
Water3,045169
1
A: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9346
Polymers60,3381
Non-polymers5965
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8725
Polymers60,3381
Non-polymers5344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7483
Polymers60,3381
Non-polymers4102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.160, 99.650, 104.300
Angle α, β, γ (deg.)110.460, 88.090, 99.720
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: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA2 - 50823 - 529
21TYRTYRBB2 - 50823 - 529
12TYRTYRAA2 - 50823 - 529
22TYRTYRCC2 - 50823 - 529
13GLUGLUBB2 - 51023 - 531
23GLUGLUCC2 - 51023 - 531

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 60337.766 Da / Num. of mol.: 3 / Fragment: BrabA.10201.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis biovar 1 (strain 1330) (bacteria)
Strain: 1330 / Gene: metG, BR0995, BS1330_I0991 / Plasmid: BrabA.10201.a.A1metG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P59078, methionine-tRNA ligase
#2: Chemical ChemComp-415 / 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea


Mass: 347.839 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H22ClN3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: BrabA.10201.a.A1.PW37326 at 21.4 mg/ml was mixed 1:1 with PACT(c2): 100 mM PCB buffer, pH=5.0, 25% (w/v) PEG-1500, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2014 / 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: 2.6→50 Å / Num. obs: 49660 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 47.423 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.12
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.6-2.672.40.472.07197.5
2.67-2.740.4342.2197.3
2.74-2.820.3322.89197.4
2.82-2.910.2723.41197.5
2.91-30.2154.32197.5
3-3.110.1755.2197.8
3.11-3.220.1386.77197.9
3.22-3.360.118.09197.1
3.36-3.510.0979.7196.1
3.51-3.680.06413.35188.9
3.68-3.880.06713.47187
3.88-4.110.05216.39190.8
4.11-4.390.04317.96197.1
4.39-4.750.03919.72197
4.75-5.20.03819.66197.7
5.2-5.810.04118.5198
5.81-6.710.03918.92197.7
6.71-8.220.0322.74197.6
8.22-11.630.02627.33197.5
11.630.02727.6190.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4LNE

4lne
PDB Unreleased entry


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.831 / SU B: 33.135 / SU ML: 0.33 / SU R Cruickshank DPI: 1.9694 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.969 / ESU R Free: 0.377
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2416 4.9 %RANDOM
Rwork0.2565 ---
obs0.258 47243 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 148.89 Å2 / Biso mean: 49.76 Å2 / Biso min: 22.51 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å20.86 Å20.37 Å2
2--1.01 Å21.78 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11165 0 104 169 11438
Biso mean--61.27 43 -
Num. residues----1445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911583
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210572
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9515764
X-RAY DIFFRACTIONr_angle_other_deg1.127324139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31351445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53123.388549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.608151672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9111585
X-RAY DIFFRACTIONr_chiral_restr0.060.21692
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113385
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022828
X-RAY DIFFRACTIONr_mcbond_it0.372.6075780
X-RAY DIFFRACTIONr_mcbond_other0.372.6075779
X-RAY DIFFRACTIONr_mcangle_it0.6833.9077213
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A53574
12B53574
21A53324
22C53324
31B53506
32C53506
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 165 -
Rwork0.333 3617 -
all-3782 -
obs--97.6 %
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)
10.3160.77820.56862.49351.13311.40860.08980.0095-0.14160.190.0886-0.2290.27090.0817-0.17840.38720.08950.01540.05510.02120.365822.6112.01121.263
20.7247-0.3286-0.60210.83590.01980.60680.0261-0.1338-0.05140.1435-0.0505-0.1111-0.05480.17260.02430.3670.0299-0.02680.0765-0.06490.437229.6388.2524.033
30.1394-0.12390.26931.35841.12272.4174-0.01890.0501-0.09250.03820.1998-0.22810.00110.4017-0.18090.3070.05470.04160.0796-0.05790.413527.16318.49421.285
41.37080.07510.35042.08060.97682.7283-0.1809-0.1667-0.0670.340.1416-0.12310.0860.06240.03930.38810.0985-0.03160.04110.00960.218721.83837.10244.33
51.4847-0.44970.58331.248-0.46940.611-0.0857-0.22750.10410.13520.07980.0927-0.0709-0.05860.00590.29560.03640.02240.0503-0.04430.11838.912-32.5835.231
610.2681-6.4472-7.01294.11654.49715.04651.47090.97241.8141-0.7007-0.5407-1.1191-0.6832-0.707-0.93021.00230.16070.28710.74150.07341.004229.223-22.36953.202
71.4221-0.66110.86040.8271-0.61221.1326-0.0482-0.03460.09730.1056-0.0675-0.0853-0.02060.01510.11570.31410.04040.00180.0345-0.03540.163519.195-33.59732.354
81.06330.00990.82940.9798-0.17042.88170.0579-0.00550.0755-0.1451-0.17670.0408-0.0208-0.17590.11880.36220.0989-0.01390.0698-0.05260.20162.562-18.9881.122
90.9961-0.48520.41631.8341-0.00560.78760.07130.0913-0.044-0.3926-0.0501-0.03640.0421-0.1026-0.02120.48540.03680.09950.0624-0.050.2093-7.6678.870.335
100.2883-1.2580.857875.0865-49.130232.197-0.58520.0986-0.08760.9096-3.6673-6.6401-0.5862.24294.25251.3872-0.23270.11751.31860.08111.0924-0.11336.19957.536
111.6214-1.01420.26772.07980.21160.97820.05740.0770.1109-0.29130.01-0.2936-0.1959-0.1746-0.06740.51610.04490.12950.0642-0.03130.2288-1.24316.29973.089
121.7901-1.35890.4732.8797-0.80090.7590.1710.1592-0.1089-0.296-0.0482-0.09010.0960.217-0.12280.45230.05130.05140.1172-0.14930.35119.001-17.65472.032
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 69
2X-RAY DIFFRACTION2A70 - 227
3X-RAY DIFFRACTION3A228 - 358
4X-RAY DIFFRACTION4A359 - 508
5X-RAY DIFFRACTION5B3 - 126
6X-RAY DIFFRACTION6B127 - 160
7X-RAY DIFFRACTION7B161 - 335
8X-RAY DIFFRACTION8B336 - 510
9X-RAY DIFFRACTION9C1 - 131
10X-RAY DIFFRACTION10C132 - 134
11X-RAY DIFFRACTION11C152 - 338
12X-RAY DIFFRACTION12C339 - 510

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