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

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Basic information

Entry
Database: PDB / ID: 4dlp
TitleCrystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis bound to selenomethionine
ComponentsAminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia
KeywordsLIGASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / class Ia aminoacyl-tRNA synthetase / selenomethionine / anomalous signal / protein synthesis / ATP-dependent
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
SELENOMETHIONINE / Methionine--tRNA ligase
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 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
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia
B: Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia
C: Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,6026
Polymers181,0133
Non-polymers5883
Water1,63991
1
A: Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5342
Polymers60,3381
Non-polymers1961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5342
Polymers60,3381
Non-polymers1961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5342
Polymers60,3381
Non-polymers1961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.250, 77.620, 116.270
Angle α, β, γ (deg.)90.00, 119.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia


Mass: 60337.766 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus 2308 (bacteria)
Gene: BAB1_1014, metG / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YQ76, methionine-tRNA ligase
#2: Chemical ChemComp-MSE / SELENOMETHIONINE


Type: L-peptide linking / Mass: 196.106 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H11NO2Se
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: BrabA.10201.a.A1 PW27667 at 28.7 mg/mL with 5 mM selenomethionine and 5 mM ATP against JCSG+ screen condition C3, 0.2 M ammonium nitrate, 20% PEG 3350, crystal tracking ID 226820c3, pH 7.5, ...Details: BrabA.10201.a.A1 PW27667 at 28.7 mg/mL with 5 mM selenomethionine and 5 mM ATP against JCSG+ screen condition C3, 0.2 M ammonium nitrate, 20% PEG 3350, crystal tracking ID 226820c3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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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: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 52724 / Num. obs: 52379 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.65-2.720.4862.6314094380999.5
2.72-2.790.4063.0514457377799.7
2.79-2.870.3443.6213960365999.8
2.87-2.960.2694.5513630357099.7
2.96-3.060.2145.7213153345299.7
3.06-3.170.1757.1312702332599.6
3.17-3.290.1369.112116320299.7
3.29-3.420.11111.0911891314899.5
3.42-3.570.09712.7310541292699.3
3.57-3.750.08215.079961283599.1
3.75-3.950.06817.799542267498.6
3.95-4.190.04624.469430255499.4
4.19-4.480.0428.39042245399.4
4.48-4.840.03531.618337226599.5
4.84-5.30.03730.727533205499.6
5.3-5.930.03829.076910188599.2
5.93-6.840.03730.756048166799.2
6.84-8.380.02739.495147142399
8.38-11.850.019483999111198.8
11.850.01848.58196959092.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å38.24 Å
Translation2.6 Å38.24 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2x1l

2x1l


Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2092 / WRfactor Rwork: 0.1737 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8368 / SU B: 23.006 / SU ML: 0.224 / SU R Cruickshank DPI: 0.7574 / SU Rfree: 0.3023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.757 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 2671 5.1 %RANDOM
Rwork0.1971 ---
obs0.1991 52379 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.74 Å2 / Biso mean: 48.2529 Å2 / Biso min: 21.88 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å2-1.21 Å2
2--3.8 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10934 0 27 91 11052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211258
X-RAY DIFFRACTIONr_bond_other_d0.0050.027352
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.94615362
X-RAY DIFFRACTIONr_angle_other_deg1.149317772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65251420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96923.346526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16151593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.081579
X-RAY DIFFRACTIONr_chiral_restr0.0750.21668
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112894
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022477
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 175 -
Rwork0.339 3500 -
all-3675 -
obs--99.59 %
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)
10.65620.0329-0.26660.0069-0.01260.5439-0.04060.0955-0.02080.00870.0060.0199-0.07320.03850.03460.0917-0.0030.01340.0670.00610.1004-3.5348-8.473837.7957
20.9554-0.06270.62050.0067-0.05821.4029-0.03960.0449-0.00650.00520.01050.00960.0840.04670.02910.08610.0222-0.0080.05130.01710.07122.0241-47.22963.4228
31.7351-0.1495-0.21280.02460.10020.68280.1118-0.2430.05260.00590.013-0.01490.10510.1012-0.12480.056-0.0233-0.00410.1486-0.02140.040326.6827-8.296686.9734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 509
2X-RAY DIFFRACTION2B2 - 508
3X-RAY DIFFRACTION3C3 - 508

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