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- PDB-5k0s: Crystal structure of methionyl-tRNA synthetase MetRS from Brucell... -

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Basic information

Entry
Database: PDB / ID: 5k0s
TitleCrystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis in complex with inhibitor Chem 1312
ComponentsMethionine--tRNA ligase
Keywordsligase/ligase inhibitor / SSGCID / MetRS / methionyl-tRNA synthetase / protein biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / LIGASE / 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-0OU / Methionine--tRNA ligase
Similarity search - Component
Biological speciesBrucella suis biovar 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.45 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: 4LNE
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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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)182,1426
Polymers181,0133
Non-polymers1,1293
Water3,945219
1
A: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7142
Polymers60,3381
Non-polymers3761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7142
Polymers60,3381
Non-polymers3761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7142
Polymers60,3381
Non-polymers3761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.270, 99.740, 104.630
Angle α, β, γ (deg.)110.580, 87.630, 99.910
Int Tables number1
Space group name H-MP1

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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-0OU / 2-({3-[(3,5-dichlorobenzyl)amino]propyl}amino)quinolin-4(1H)-one


Mass: 376.280 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H19Cl2N3O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
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(d2): 100 mM MMT 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: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 9, 2013
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 63652 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 40.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.43
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.4-2.462.40.5252.13185.2
2.46-2.530.4522.51197.4
2.53-2.60.3722.98197.6
2.6-2.680.2853.87197.4
2.68-2.770.2474.19197.7
2.77-2.870.2055.09197.7
2.87-2.980.1596.4198
2.98-3.10.1257.85197.9
3.1-3.240.09310.05197.9
3.24-3.390.07611.7198.1
3.39-3.580.06214.03198.1
3.58-3.790.04221.24190.6
3.79-4.060.04220.94194
4.06-4.380.03322.78198.2
4.38-4.80.02724.82198.7
4.8-5.370.02923.48198.2
5.37-6.20.03522.24198.8
6.2-7.590.02724.97198.6
7.59-10.730.01932.05198.6
10.730.01934.35187.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2405refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4DLP
Resolution: 2.45→34.925 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.43
RfactorNum. reflection% reflection
Rfree0.2556 3027 5.01 %
Rwork0.2102 --
obs0.2125 60396 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.76 Å2 / Biso mean: 43.2893 Å2 / Biso min: 20.61 Å2
Refinement stepCycle: final / Resolution: 2.45→34.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11444 0 75 219 11738
Biso mean--49.72 41.76 -
Num. residues----1478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311859
X-RAY DIFFRACTIONf_angle_d0.57716178
X-RAY DIFFRACTIONf_chiral_restr0.041729
X-RAY DIFFRACTIONf_plane_restr0.0042127
X-RAY DIFFRACTIONf_dihedral_angle_d11.9036957
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.48820.31121480.25492629277797
2.4882-2.5290.32171330.24692604273797
2.529-2.57260.2681260.23942610273698
2.5726-2.61940.29951340.24182619275398
2.6194-2.66970.33871490.24152652280198
2.6697-2.72420.28171410.24062555269698
2.7242-2.78340.2641360.22392623275998
2.7834-2.84810.2661460.22752667281398
2.8481-2.91930.31611130.21682604271798
2.9193-2.99820.28181420.22732650279298
2.9982-3.08640.24461410.23252591273298
3.0864-3.18590.26191420.22452622276498
3.1859-3.29970.31171510.24432641279298
3.2997-3.43170.30181570.26512602275998
3.4317-3.58780.25361260.23352624275098
3.5878-3.77670.41441200.33882439255990
3.7767-4.0130.27451260.22832502262894
4.013-4.32240.18951550.15732611276699
4.3224-4.75640.16251530.13372605275899
4.7564-5.44240.18251430.14512655279899
5.4424-6.84840.21341380.16782650278899
6.8484-34.92890.16831070.14012614272196
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.33320.3010.1910.38010.57321.75370.019-0.00970.00890.04150.062-0.09790.1490.0062-0.08370.28890.0382-0.01710.27580.04440.387120.96429.394618.0632
21.2973-1.6810.97424.53940.18533.66480.40910.1387-0.2346-0.466-0.3645-0.9315-0.511-0.13510.00430.2877-0.0384-0.07520.31760.0880.514348.40971.5527-4.3877
31.11310.0928-0.12721.67211.26182.2014-0.07840.1032-0.0207-0.1130.1943-0.2358-0.26290.2767-0.11780.2469-0.0570.00550.2773-0.010.286524.834314.93486.4032
41.3307-0.4039-0.17032.06011.06881.6726-0.0922-0.1123-0.19020.2810.172-0.18040.13280.2112-0.1070.32710.0313-0.06570.35230.0520.329124.95533.328842.5536
52.2692-0.93770.79251.355-1.19211.2595-0.0606-0.31080.04070.01260.1990.109-0.0145-0.2936-0.13390.2292-0.0399-0.0440.2896-0.03280.28698.4728-32.832234.5637
61.69321.2511-0.18175.96-0.77933.00290.70290.05860.55790.9018-0.75740.71660.01570.07170.080.6765-0.02140.18250.5047-0.10350.582930.791-24.150453.3291
71.1061-0.93990.75972.0376-1.23291.5517-0.0475-0.03270.0289-0.011-0.0433-0.0777-0.0283-0.07530.10010.2603-0.016-0.02880.2958-0.01220.246319.3191-33.874732.5447
81.306-0.02110.68461.4550.06723.04090.11660.0278-0.0133-0.2267-0.16350.09410.0915-0.16280.03450.25540.0086-0.02640.304-0.00210.27313.1711-19.07641.4747
90.7792-0.41560.20950.98880.97181.5274-0.05920.1224-0.1969-0.1593-0.00160.13770.0476-0.17050.03610.4333-0.09260.1120.34060.0080.3597-7.34967.524170.9409
102.4091.0185-1.5132.06450.00061.9691-0.27440.30340.2432-0.25680.3419-0.4195-0.2703-0.5108-0.02350.5177-0.02510.02550.68090.13940.5065-3.846136.121755.9706
111.6939-0.77210.31062.79990.47272.18580.02390.1015-0.029-0.24440.0274-0.2414-0.1855-0.0383-0.06030.4017-0.01290.12120.24380.00430.2513-2.235417.85376.248
121.9918-1.38980.41061.7137-0.86451.27670.22470.2416-0.0746-0.3623-0.18-0.01790.09930.2512-0.04880.4009-0.02560.03560.2912-0.06110.333618.643-15.650270.8276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:122)A3 - 122
2X-RAY DIFFRACTION2(chain A and resid 123:159)A123 - 159
3X-RAY DIFFRACTION3(chain A and resid 160:311)A160 - 311
4X-RAY DIFFRACTION4(chain A and resid 312:508)A312 - 508
5X-RAY DIFFRACTION5(chain B and resid 3:122)B3 - 122
6X-RAY DIFFRACTION6(chain B and resid 123:162)B123 - 162
7X-RAY DIFFRACTION7(chain B and resid 163:331)B163 - 331
8X-RAY DIFFRACTION8(chain B and resid 332:509)B332 - 509
9X-RAY DIFFRACTION9(chain C and resid 3:124)C3 - 124
10X-RAY DIFFRACTION10(chain C and resid 125:162)C125 - 162
11X-RAY DIFFRACTION11(chain C and resid 163:313)C163 - 313
12X-RAY DIFFRACTION12(chain C and resid 314:510)C314 - 510

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