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- PDB-7k9m: Crystal structure of the complex of M. tuberculosis PheRS with co... -

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Basic information

Entry
Database: PDB / ID: 7k9m
TitleCrystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and 5'-O-(N-phenylalanyl)sulfamoyl-adenosine
Components
  • (Phenylalanine--tRNA ligase ...) x 2
  • tRNA(Phe)
KeywordsLIGASE/RNA / aminoacylation / phenylalanyl tRNA synthetase / adenylate analog / LIGASE-RNA complex / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / peptidoglycan-based cell wall / tRNA binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain ...Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / B3/4 domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / B3/4 domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Putative DNA-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / 3-Layer(bba) Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / 5'-O-(L-phenylalanylsulfamoyl)adenosine / : / RNA / RNA (> 10) / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMichalska, K. / Chang, C. / Jedrzejczak, R. / Wower, J. / Baragana, B. / Forte, B. / Gilbert, I.H. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation.
Authors: Michalska, K. / Jedrzejczak, R. / Wower, J. / Chang, C. / Baragana, B. / Gilbert, I.H. / Forte, B. / Joachimiak, A.
History
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 16, 2021Group: Database references / Category: pdbx_database_related
Revision 1.3Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
C: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,76916
Polymers151,1253
Non-polymers1,64413
Water5,801322
1
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
C: tRNA(Phe)
hetero molecules

A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
C: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,53832
Polymers302,2516
Non-polymers3,28726
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area35210 Å2
ΔGint-187 kcal/mol
Surface area112620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.432, 110.753, 147.897
Angle α, β, γ (deg.)90.000, 103.590, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Phenylalanine--tRNA ligase ... , 2 types, 2 molecules AB

#1: Protein Phenylalanine--tRNA ligase alpha subunit / Phenylalanyl-tRNA synthetase alpha subunit / PheRS


Mass: 37415.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pheS, Rv1649, MTCY06H11.14 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: P9WFU3, phenylalanine-tRNA ligase
#2: Protein Phenylalanine--tRNA ligase beta subunit / Phenylalanyl-tRNA synthetase beta subunit / PheRS


Mass: 88867.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pheT, Rv1650, MTCY06H11.15 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: P9WFU1, phenylalanine-tRNA ligase

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RNA chain , 1 types, 1 molecules C

#3: RNA chain tRNA(Phe)


Mass: 24842.811 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
References: GenBank: 1251771558

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Non-polymers , 6 types, 335 molecules

#4: Chemical ChemComp-W5Y / 5'-O-(L-phenylalanylsulfamoyl)adenosine


Mass: 493.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O7S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium sodium tartrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 68621 / % possible obs: 99 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.073 / Rrim(I) all: 0.186 / Χ2: 0.935 / Net I/σ(I): 5.5 / Num. measured all: 427793
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.90.83232740.5220.4650.9590.95496.2
2.54-2.594.30.80433750.5740.4280.9160.93797.2
2.59-2.645.10.80134620.6220.3930.8960.93999.6
2.64-2.695.50.75133980.6710.3580.8340.94999.6
2.69-2.755.90.71934480.7180.3280.7920.93999.7
2.75-2.826.20.66634550.7820.2930.7290.96299.7
2.82-2.896.40.59434000.8370.2560.6480.96599.7
2.89-2.966.50.55134640.8680.2340.60.97399.6
2.96-3.056.50.45434180.9160.1910.4940.98198.7
3.05-3.1560.38233620.9360.1640.417197.1
3.15-3.266.90.31434360.9550.1280.340.98899.5
3.26-3.3970.25234690.9730.1030.2730.99299.7
3.39-3.556.90.19634440.9790.0810.2121.00299.9
3.55-3.736.90.15734410.9860.0640.171.00399.6
3.73-3.976.70.12434490.9890.0510.1350.97399.3
3.97-4.276.40.09634130.9930.040.1040.94898
4.27-4.77.10.0834790.9950.0320.0860.92699.9
4.7-5.3870.07534530.9950.030.0810.84599.2
5.38-6.786.50.0734360.9950.0290.0760.74498.4
6.78-506.80.04435450.9980.0180.0480.7199.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
SBC-Collectdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7KA0

7ka0


Resolution: 2.5→47.92 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 3264 4.9 %
Rwork0.1793 63320 -
obs0.181 66584 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.21 Å2 / Biso mean: 56.7561 Å2 / Biso min: 11.01 Å2
Refinement stepCycle: final / Resolution: 2.5→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8861 1413 108 322 10704
Biso mean--54.38 36.99 -
Num. residues----1239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.540.33681110.26362087219874
2.54-2.580.27611270.23962317244481
2.58-2.620.30821210.23232473259487
2.62-2.670.25521390.21662619275891
2.67-2.720.25221250.21182719284495
2.72-2.770.26061580.21322755291397
2.77-2.830.24751540.21772835298998
2.83-2.890.25211480.2222769291799
2.89-2.950.26661400.22052881302199
2.95-3.030.26731290.21472832296198
3.03-3.110.27031560.21092755291197
3.11-3.20.23091410.2082805294698
3.2-3.30.22031580.20832841299999
3.3-3.420.24331550.20328553010100
3.42-3.560.22231250.187628893014100
3.56-3.720.21441500.171428513001100
3.72-3.920.18081470.16352847299499
3.92-4.160.16281650.14962796296198
4.16-4.480.17631450.137728833028100
4.48-4.930.18171470.130328743021100
4.93-5.650.17941410.15132864300599
5.65-7.110.20661180.16752888300698
7.11-47.920.18311640.15632885304998
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)
10.9050.29250.76080.8590.90022.73270.44380.4991-0.36980.1306-0.1221-0.36871.177-0.3554-0.26140.9655-0.0082-0.27650.8534-0.16720.9201-69.8014-1.5458109.2149
20.2655-0.0787-0.13880.0441-0.0660.62810.00470.2921-0.1881-0.23450.10140.01140.2404-0.1578-0.03770.4207-0.1299-0.05880.4423-0.01730.3881-63.065713.9604123.068
30.61340.3019-0.09471.01280.13750.58830.0591-0.04310.02610.0854-0.045-0.0368-0.07610.01670.00030.1767-0.02960.02340.2153-0.01510.223-26.216763.2433162.7776
40.69950.0379-0.23390.6394-0.77091.2054-0.0318-0.2722-0.22880.36590.16070.0102-0.1054-0.2579-0.12570.70810.02610.070.50420.05780.3932-35.968765.2452207.3485
50.3811-0.4105-0.17880.57510.33381.389-0.1326-0.24620.07870.5320.1361-0.2757-0.11640.1104-0.00080.67720.0225-0.04490.3744-0.06850.3523-22.135980.3748195.7379
60.99350.1137-0.07610.98850.33841.3254-0.0657-0.31590.09190.57570.0736-0.306-0.16020.27580.0050.6219-0.0041-0.11110.3847-0.08970.384-13.844580.5271189.7521
70.2752-0.01260.01860.63680.26470.4260.0870.0069-0.0642-0.0172-0.0637-0.13820.03290.0329-0.03040.15870.00730.01860.21660.00610.2527-18.14236.0242145.0669
81.90720.33621.54370.5460.74161.70960.23380.01340.0630.5-0.0029-0.3525-0.22840.2054-0.31321.22230.0091-0.16751.35760.0580.9268-53.416518.442297.2116
90.51010.0462-0.28370.0264-0.0210.1591-0.59990.4142-0.5272-0.1048-0.27390.02930.23470.0680.7061.679-0.1276-0.6541.7884-0.03341.3461-52.62037.907799.641
100.19740.37210.42090.71320.81120.92351.11490.9046-1.4416-0.83810.03430.93280.963-0.5243-0.81091.00510.1007-0.51721.1882-0.08651.1117-38.23238.4026115.5243
110.2952-0.73370.23362.68050.79213.1728-0.2572-1.17620.8242-0.0238-0.2442-0.1684-0.4991-0.79750.43031.28010.0895-0.19071.3345-0.08611.1248-66.901624.328296.5875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 52 )A3 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 110 )A53 - 110
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 341 )A111 - 341
4X-RAY DIFFRACTION4chain 'B' and (resid -3 through 131 )B-3 - 131
5X-RAY DIFFRACTION5chain 'B' and (resid 132 through 231 )B132 - 231
6X-RAY DIFFRACTION6chain 'B' and (resid 232 through 486 )B232 - 486
7X-RAY DIFFRACTION7chain 'B' and (resid 487 through 831 )B487 - 831
8X-RAY DIFFRACTION8chain 'C' and (resid 5 through 19 )C5 - 19
9X-RAY DIFFRACTION9chain 'C' and (resid 20 through 24 )C20 - 24
10X-RAY DIFFRACTION10chain 'C' and (resid 25 through 49 )C25 - 49
11X-RAY DIFFRACTION11chain 'C' and (resid 50 through 70 )C50 - 70

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