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- PDB-7kab: M. tuberculosis PheRS complex with cognate precursor tRNA and phe... -

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Basic information

Entry
Database: PDB / ID: 7kab
TitleM. tuberculosis PheRS complex with cognate precursor tRNA and phenylalanine
Components
  • (Phenylalanine--tRNA ligase ...) x 2
  • tRNA(Phe)
KeywordsLIGASE/RNA / aminoacylation / phenylalanyl tRNA synthetase / Structural Genomics / Ligase-tRNA complex / Center for Structural Genomics of Infectious Diseases / CSGID / LIGASE-RNA complex
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
S-1,2-PROPANEDIOL / R-1,2-PROPANEDIOL / PHENYLALANINE / : / 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
AuthorsChang, C. / Michalska, K. / Jedrzejczak, R. / Wower, J. / 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 30, 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)152,21022
Polymers151,1253
Non-polymers1,08519
Water2,702150
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)304,42144
Polymers302,2516
Non-polymers2,17038
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area35020 Å2
ΔGint-321 kcal/mol
Surface area112820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.597, 110.452, 148.413
Angle α, β, γ (deg.)90.000, 105.070, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1002-

HOH

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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 / 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 / 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 , 7 types, 169 molecules

#4: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 14.3% PEG20000, 0.15 M TAPS, 5.0% 1,2-propanediol

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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: Dec 9, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 68179 / % possible obs: 99.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.057 / Rrim(I) all: 0.153 / Χ2: 1.167 / Net I/σ(I): 5.1 / Num. measured all: 477367
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.91.37434040.4870.611.5070.44999.4
2.54-2.596.21.28633760.5930.5521.4020.45999.4
2.59-2.646.61.18534340.6660.4911.2840.4799.6
2.64-2.696.81.08633770.650.4451.1760.48699.4
2.69-2.7570.99634000.7520.4041.0770.49899.5
2.75-2.8270.83734190.8310.3370.9040.52399.5
2.82-2.896.90.67433840.8440.2740.7290.55599
2.89-2.966.40.56133250.8210.2380.6110.59297.6
2.96-3.057.40.44834230.930.1750.4820.63799.8
3.05-3.157.40.35734030.9570.1390.3840.70499.6
3.15-3.267.40.30234170.9710.1180.3250.75799.7
3.26-3.397.30.2334170.9810.090.2470.86599.8
3.39-3.557.30.18434490.9840.0730.1981.0899.8
3.55-3.737.10.14733600.9880.0590.1581.28699.2
3.73-3.976.80.12233720.990.050.1321.59298.1
3.97-4.277.60.10634400.9930.0410.1141.89799.8
4.27-4.77.50.09634390.9930.0370.1032.26399.7
4.7-5.387.30.08934190.9940.0350.0962.19499.2
5.38-6.767.10.08334290.9930.0330.0892.26298.6
6.76-307.20.06134920.9960.0250.0663.14199.1

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Processing

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

7ka0


Resolution: 2.5→29.69 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 1665 2.44 %
Rwork0.186 66452 -
obs0.1866 68117 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 287.13 Å2 / Biso mean: 99.5524 Å2 / Biso min: 25.54 Å2
Refinement stepCycle: final / Resolution: 2.5→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8792 1413 65 150 10420
Biso mean--87.16 61.43 -
Num. residues----1236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.570.33181370.28855404554197
2.57-2.660.30371360.25625526566299
2.66-2.750.28771360.24885532566899
2.75-2.860.28841260.23125525565199
2.86-2.990.24391400.23735465560598
2.99-3.150.27471360.218855735709100
3.15-3.350.24951480.215555465694100
3.35-3.60.2371380.200155635701100
3.6-3.970.20051630.17725479564298
3.97-4.540.18761300.15856075737100
4.54-5.710.16551290.15655565569499
5.71-29.690.17831460.15965667581399
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)
10.0023-0.0051-0.00460.00870.00680.0140.2330.1420.13730.24880.0544-0.0421-0.18970.0379-02.4609-0.0719-0.38582.5972-0.02152.0425-56.490318.292697.088
20.00120.0021-0.00530.01150.00260.00890.06280.1133-0.0856-0.02820.03860.0606-0.08520.042302.7195-0.0701-0.59872.2178-0.21032.1005-49.951310.3905105.8912
3-0.0006-0.00410.00160.01690.00860.00410.47860.2395-0.2635-0.07660.2643-0.00870.058-0.03830.00011.14060.0763-0.31390.8809-0.05670.8719-33.91425.7385122.9717
40.00550.0032-0.00780.00830.01520.02720.16020.0642-0.14420.06860.36840.21570.1793-0.0591-0.00012.16360.2155-0.74232.2965-0.38961.8252-49.19257.9252109.653
50.0026-0.00710.00320.0182-0.00650.00050.0983-0.00270.0015-0.0118-0.062-0.06020.0051-0.067-01.72060.035-0.30332.70940.08372.1852-74.549819.995797.227
60.0113-0.00040.01480.0166-0.00770.00920.1442-0.06640.2812-0.0819-0.1184-0.1777-0.0335-0.140202.34080.1853-0.38382.19570.27791.9484-64.731128.545995.1311
70.0243-0.0190.01490.0075-0.00550.0049-0.01190.2831-0.10220.22910.0827-0.2070.2806-0.017701.5662-0.3308-0.13141.5731-0.30331.2947-73.2357-1.617108.8071
80.11790.10280.13870.19010.11690.69810.1168-0.0741-0.03070.1316-0.0751-0.0294-0.0286-0.03210.00130.2304-0.03220.03760.3567-0.01580.4198-37.07249.8744151.1871
90.49040.4578-0.16350.6225-0.52510.99960.0841-0.1296-0.30680.3994-0.10720.2528-0.4738-0.0079-0.0770.40490.01380.16570.4248-0.1070.6337-40.117568.5812167.3468
100.268-0.08940.04040.05520.05020.1779-0.0195-0.04430.08070.10350.05190.1435-0.0448-0.0763-00.378-0.06380.01310.4274-0.01170.4738-32.701159.6663161.5156
118.98762.00112.002822.00022.00060.16250.0152-0.1657-0.15580.14550.44920.2938-0.0516-0.31040.4855-0.06760.02610.7826-0.28210.8478-28.759866.5014165.222
120.26190.2111-0.05770.0554-0.07370.02750.1416-0.0111-0.17880.36090.1527-0.0559-0.406-0.18190.01221.11860.06290.08860.62290.07030.4996-41.451667.102204.9095
130.46610.32630.14960.5631-0.18270.2212-0.04080.2337-0.09560.83840.42410.1671-0.5867-0.03710.70851.27820.0573-0.00860.3443-0.17670.2987-29.397376.7051199.4039
140.2505-0.1919-0.0540.4605-0.03380.3-0.2102-0.11290.16690.70710.1843-0.565-0.05880.0212-0.06581.3206-0.0452-0.32680.7005-0.14990.5836-13.853376.5819196.2536
150.13150.05590.06290.88440.18850.61380.07860.0129-0.04910.0361-0.0699-0.1676-0.07450.088400.2523-0.04260.01260.3376-0.01020.348-23.609954.0387157.5319
160.559-0.1820.01230.3882-0.09750.16620.11820.1483-0.0913-0.0783-0.1162-0.13460.07850.0832-00.39430.09550.02220.4059-0.04990.4285-23.399924.4843128.9429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 5 through 19 )C5 - 19
2X-RAY DIFFRACTION2chain 'C' and (resid 20 through 29 )C20 - 29
3X-RAY DIFFRACTION3chain 'C' and (resid 30 through 39 )C30 - 39
4X-RAY DIFFRACTION4chain 'C' and (resid 40 through 49 )C40 - 49
5X-RAY DIFFRACTION5chain 'C' and (resid 50 through 59 )C50 - 59
6X-RAY DIFFRACTION6chain 'C' and (resid 60 through 70 )C60 - 70
7X-RAY DIFFRACTION7chain 'A' and (resid 4 through 56 )A4 - 56
8X-RAY DIFFRACTION8chain 'A' and (resid 57 through 242 )A57 - 242
9X-RAY DIFFRACTION9chain 'A' and (resid 243 through 285 )A243 - 285
10X-RAY DIFFRACTION10chain 'A' and (resid 286 through 341 )A286 - 341
11X-RAY DIFFRACTION11chain 'A' and (resid 501 through 501 )A501
12X-RAY DIFFRACTION12chain 'B' and (resid -3 through 113 )B-3 - 113
13X-RAY DIFFRACTION13chain 'B' and (resid 114 through 241 )B114 - 241
14X-RAY DIFFRACTION14chain 'B' and (resid 242 through 418 )B242 - 418
15X-RAY DIFFRACTION15chain 'B' and (resid 419 through 700 )B419 - 700
16X-RAY DIFFRACTION16chain 'B' and (resid 701 through 831 )B701 - 831

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