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- PDB-4eg3: Trypanosoma brucei methionyl-tRNA synthetase in complex with prod... -

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Basic information

Entry
Database: PDB / ID: 4eg3
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with product methionyl-adenylate
ComponentsMethionyl-tRNA synthetase, putativeMethionine—tRNA ligase
KeywordsLIGASE / aminoacyl-tRNA synthetase / aaRS / MetRS / parasite / protein-inhibitor complex / Rossmann-fold / translation / nucleotide binding / Rossmann Fold / tRNA binding ATP binding
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ciliary plasm / 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 / 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-ME8 / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.94 Å
AuthorsKoh, C.Y. / Kim, J.E. / Shibata, S. / Fan, E. / Verlinde, C.L.M.J. / Hol, W.G.J.
CitationJournal: Structure / Year: 2012
Title: Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection.
Authors: Koh, C.Y. / Kim, J.E. / Shibata, S. / Ranade, R.M. / Yu, M. / Liu, J. / Gillespie, J.R. / Buckner, F.S. / Verlinde, C.L. / Fan, E. / Hol, W.G.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionyl-tRNA synthetase, putative
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,83915
Polymers122,8692
Non-polymers1,97013
Water1,856103
1
A: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5589
Polymers61,4351
Non-polymers1,1238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2826
Polymers61,4351
Non-polymers8475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.477, 105.908, 208.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methionyl-tRNA synthetase, putative / Methionine—tRNA ligase


Mass: 61434.707 Da / Num. of mol.: 2 / Fragment: RESIDUES 235-773 / Mutation: K452A, K453R, E454A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb10.70.6470 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38C91, methionine-tRNA ligase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ME8 / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanyl-4-methylsulfanyl-butanoate / L-methionine-AMP / methionyl-adenylate


Mass: 478.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N6O8PS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.84 Å3/Da / Density % sol: 67.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.0 to 2.3M ammonium sulfate, 0.2M sodium chloride and 0.1M sodium cacodylate pH 6.0 to 6.6, vapor diffusion, sitting drop, temperature 298K
PH range: 6.0 to 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 15, 2010
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 40932 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.192 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.94-3.066.41100
3.06-3.186.411000.802
3.18-3.326.411000.592
3.32-3.56.411000.431
3.5-3.726.311000.301
3.72-46.311000.233
4-4.416.311000.179
4.41-5.046.311000.139
5.04-6.356.611000.141
6.35-506.8198.90.072

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.67 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.94 Å44 Å
Translation2.94 Å44 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.6.0117refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.94→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 37.27 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R: 0.938 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26644 2045 5 %RANDOM
Rwork0.2116 ---
obs0.21435 38631 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.97 Å2
Baniso -1Baniso -2Baniso -3
1-9.88 Å20 Å20 Å2
2---5.2 Å20 Å2
3----4.68 Å2
Refinement stepCycle: LAST / Resolution: 2.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8435 0 128 103 8666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.028773
X-RAY DIFFRACTIONr_bond_other_d0.0010.025984
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.96911911
X-RAY DIFFRACTIONr_angle_other_deg0.811314527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67751051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6923.434396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.229151429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.531558
X-RAY DIFFRACTIONr_chiral_restr0.0590.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021851
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.94→3.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 145 -
Rwork0.363 2471 -
obs--94.47 %
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)
11.2518-0.5634-0.61761.46890.65180.60730.03780.0716-0.0405-0.3526-0.0703-0.04530.0435-0.13330.03250.2653-0.02290.06230.1297-0.00480.0369-3.24-16.952-53.687
21.1603-0.8639-1.04943.2091-0.26941.919-0.03940.1522-0.0563-0.5937-0.00640.11370.0979-0.28570.04580.2276-0.0364-0.01250.1958-0.02320.1116-4.398-9.779-51.347
31.3424-0.76-0.85353.2341.49482.21640.1425-0.0043-0.191-0.321-0.14730.4151-0.3756-0.39930.00490.06630.0567-0.00990.23560.00230.1132-26.748.096-34.021
41.24460.0317-0.72352.1229-0.25012.7346-0.1681-0.2298-0.12620.35970.15660.04630.19320.05090.01140.09520.06480.01560.1017-0.00580.0887-26.499.62110.811
54.37330.25750.04573.1155-0.82962.4798-0.0393-0.0491-0.2267-0.10060.29620.6203-0.0154-0.4664-0.25690.2070.08390.01020.1570.06920.1639-46.18721.90811.672
61.9403-1.2016-0.34542.16990.37852.3782-0.001-0.01190.10570.28750.08370.0063-0.0321-0.1097-0.08270.14690.01740.02490.1283-0.01560.0831-33.63923.5266.11
71.9492-0.9731-0.70521.64690.55612.1354-0.19090.0062-0.20740.31520.07770.11850.34540.08230.11310.18730.00010.02880.1295-0.01730.1155-13.533-4.155-9.714
89.5884-5.22515.88438.92-4.53213.92770.41320.43-1.30591.01890.26810.27650.03810.2332-0.68130.59860.25370.02770.2898-0.05440.3053-15.819-17.708-2.962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A239 - 470
2X-RAY DIFFRACTION2A471 - 563
3X-RAY DIFFRACTION3A564 - 767
4X-RAY DIFFRACTION4B-4 - 334
5X-RAY DIFFRACTION5B335 - 402
6X-RAY DIFFRACTION6B403 - 546
7X-RAY DIFFRACTION7B547 - 754
8X-RAY DIFFRACTION8B755 - 768

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