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- PDB-4zt4: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

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Entry
Database: PDB / ID: 4zt4
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitorN-(3,5-dichlorobenzyl)-2,2-difluoro-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1708)
ComponentsMethionyl-tRNA synthetase
KeywordsLigase/Ligase Inhibitor / ligase / aminoacyl-tRNA synthetase / aaRS / MetRS / Trypanosoma brucei / protein-inhibitor complex / Ligase-Ligase Inhibitor complex
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ciliary plasm / mitochondrion / 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-4RO / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKoh, C.-Y. / Hol, W.G.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acs Infect Dis. / Year: 2016
Title: 5-Fluoroimidazo[4,5-b]pyridine Is a Privileged Fragment That Conveys Bioavailability to Potent Trypanosomal Methionyl-tRNA Synthetase Inhibitors.
Authors: Zhang, Z. / Koh, C.Y. / Ranade, R.M. / Shibata, S. / Gillespie, J.R. / Hulverson, M.A. / Huang, W. / Nguyen, J. / Pendem, N. / Gelb, M.H. / Verlinde, C.L. / Hol, W.G. / Buckner, F.S. / Fan, E.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Jan 15, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,8279
Polymers122,8692
Non-polymers9587
Water7,837435
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8185
Polymers61,4351
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0094
Polymers61,4351
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.516, 106.128, 207.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methionyl-tRNA synthetase


Mass: 61434.707 Da / Num. of mol.: 2 / Fragment: UNP residues 237-773 / Mutation: K456A, K457R, E458A
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

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Non-polymers , 6 types, 442 molecules

#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-4RO / N-(3,5-dichlorobenzyl)-2,2-difluoro-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine


Mass: 386.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15Cl2F2N5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.91 Å3/Da / Density % sol: 68.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.0-2.3 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M sodium cacodylate
PH range: 6.0 to 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.954 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2014
RadiationMonochromator: Liquid nitrogen-cooled double crystal, Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.3→38.59 Å / Num. obs: 86315 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.041 / Net I/σ(I): 17 / Num. measured all: 583582
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.346.90.9952.23107545000.7420.406100
12.17-38.596.30.01957.8416166310.00897.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.68 Å38.59 Å
Translation8.68 Å38.59 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
REFMACrefmac_5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EG8

4eg8


Resolution: 2.3→38.59 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / Matrix type: sparse / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.2 / SU B: 12.13 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 4315 5 %RANDOM
Rwork0.2004 81926 --
obs0.2016 81926 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.64 Å2 / Biso mean: 44.603 Å2 / Biso min: 22.25 Å2
Baniso -1Baniso -2Baniso -3
1-3.83 Å2-0 Å20 Å2
2---1.74 Å2-0 Å2
3----2.08 Å2
Refinement stepCycle: final / Resolution: 2.3→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8226 0 57 435 8718
Biso mean--60.73 44.31 -
Num. residues----1048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198510
X-RAY DIFFRACTIONr_bond_other_d0.0030.027957
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.95211585
X-RAY DIFFRACTIONr_angle_other_deg0.881318259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.26151048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49723.298376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.306151329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9281554
X-RAY DIFFRACTIONr_chiral_restr0.0620.21289
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219642
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021978
X-RAY DIFFRACTIONr_mcbond_it1.132.9814195
X-RAY DIFFRACTIONr_mcbond_other1.132.9814194
X-RAY DIFFRACTIONr_mcangle_it1.9114.4655237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.3-2.360.3273000.3025987629099.9520.302
2.36-2.4240.312900.2875821611699.9180.287
2.424-2.4940.2982940.2715672598199.7490.271
2.494-2.570.2962890.2485466576499.8440.248
2.57-2.6540.2582710.235399567599.9120.23
2.654-2.7470.2412880.2235163545599.9270.223
2.747-2.850.2732550.2114988524799.9240.211
2.85-2.9660.2242650.2064792506199.9210.206
2.966-3.0970.272430.2064638488999.8360.206
3.097-3.2470.2452450.24442469199.9150.2
3.247-3.4210.2132310.1944210444599.910.194
3.421-3.6270.1982010.1854019422299.9530.185
3.627-3.8750.21940.1813771397299.8240.181
3.875-4.1820.1992050.1743513373099.6780.174
4.182-4.5760.1831880.1583247343799.9420.158
4.576-5.1070.1721630.1592967313699.8090.159
5.107-5.880.2061210.1952637277199.5310.195
5.88-7.160.2031130.219228523981000.219
7.16-9.9550.181970.1691794190199.4740.169
9.955-38.5860.294620.2251114117799.9150.225
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)
11.405-0.5625-0.74922.13390.98822.0380.08940.3-0.1302-0.1934-0.20430.11930.0455-0.27180.11490.0760.02080.02330.0945-0.03210.0714-11.471-7.057-56.683
21.2806-0.5706-0.67041.9070.57621.4717-0.06650.0486-0.0639-0.02160.01060.03380.0762-0.07160.05590.0433-0.01610.05570.0316-0.02870.11072.211-16.759-51.482
31.3799-1.2088-0.19091.72821.96145.43120.09390.3238-0.48370.184-0.34450.33311.0136-0.22480.25060.3588-0.01650.08890.2493-0.15960.5494-24.606-10.999-44.659
41.3126-0.6047-0.47321.80430.3621.5985-0.01190.0687-0.09080.0665-0.03470.2681-0.1389-0.36490.04670.0380.02430.04990.1118-0.01180.1258-27.2311.293-32.111
50.7390.27960.26269.53321.30371.26510.20710.16010.143-0.4065-0.26941.31460.1429-0.57420.06230.2323-0.025-0.00420.39350.06350.2365-31.61512.988-39.159
60.997-0.483-0.45980.46570.55341.2091-0.1303-0.1317-0.08090.15070.07640.14410.0353-0.06260.05390.14750.0530.0760.06970.03250.1272-32.73513.70110.973
77.03881.39823.58251.682-2.788418.53660.1390.1527-0.0595-0.21770.01020.27590.5198-0.0067-0.14920.44390.0777-0.07980.2424-0.03720.3696-61.50115.8629.501
81.0808-0.5393-0.39370.77380.40551.85670.00020.0202-0.01280.1530.00470.0205-0.1353-0.1952-0.00490.12030.05850.08310.08190.02970.1303-38.23422.8695.081
91.1811-0.2958-0.50031.32420.19871.6857-0.1008-0.0253-0.22030.18520.01640.14540.25260.03140.08440.1080.00930.05610.0414-0.01090.1353-16.089-4.156-10.366
106.08042.5635-0.15612.78050.70141.51070.1306-0.6001-0.92090.4992-0.0966-0.16650.52480.1763-0.0340.26350.0527-0.02110.12440.05130.2846-7.831-9.073-6.098
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 337
2X-RAY DIFFRACTION2A338 - 546
3X-RAY DIFFRACTION3A547 - 593
4X-RAY DIFFRACTION4A594 - 740
5X-RAY DIFFRACTION5A741 - 767
6X-RAY DIFFRACTION6B-4 - 362
7X-RAY DIFFRACTION7B363 - 398
8X-RAY DIFFRACTION8B399 - 546
9X-RAY DIFFRACTION9B547 - 741
10X-RAY DIFFRACTION10B742 - 767

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