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- PDB-8c9e: Priestia megaterium mupirocin-sensitive isoleucyl-tRNA synthetase... -

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Basic information

Entry
Database: PDB / ID: 8c9e
TitlePriestia megaterium mupirocin-sensitive isoleucyl-tRNA synthetase 1 complexed with an isoleucyl-adenylate analogue
ComponentsIsoleucine--tRNA ligase
KeywordsRNA BINDING PROTEIN / antibiotic / mupirocin-sensitive / IleRS1
Function / homology
Function and homology information


isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / tRNA binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
: / Isoleucine-tRNA ligase, type 1 / Isoleucyl tRNA synthetase type 1, anticodon-binding domain / Isoleucine-tRNA ligase / Zinc finger, FPG/IleRS-type / Zinc finger found in FPG and IleRS / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding ...: / Isoleucine-tRNA ligase, type 1 / Isoleucyl tRNA synthetase type 1, anticodon-binding domain / Isoleucine-tRNA ligase / Zinc finger, FPG/IleRS-type / Zinc finger found in FPG and IleRS / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
N-[ISOLEUCINYL]-N'-[ADENOSYL]-DIAMINOSUFONE / : / Isoleucine--tRNA ligase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBrkic, A. / Leibundgut, M. / Jablonska, J. / Zanki, V. / Car, Z. / Petrovic Perokovic, V. / Ban, N. / Gruic-Sovulj, I.
Funding support Croatia, Switzerland, European Union, 3items
OrganizationGrant numberCountry
Croatian Science Foundation180567 Croatia
Swiss National Science Foundation180567 Switzerland
European Regional Development FundKK.01.1.1.02.0016European Union
CitationJournal: Nat Commun / Year: 2023
Title: Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif.
Authors: Brkic, A. / Leibundgut, M. / Jablonska, J. / Zanki, V. / Car, Z. / Petrovic Perokovic, V. / Marsavelski, A. / Ban, N. / Gruic-Sovulj, I.
History
DepositionJan 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Mar 27, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoleucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,96319
Polymers105,0911
Non-polymers1,87318
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, The nonhydrolyzable isoleucyl-adenylate analogue is known to bind close homologs of the studied enzymes.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-139 kcal/mol
Surface area40480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.090, 127.090, 163.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Isoleucine--tRNA ligase / Isoleucyl-tRNA synthetase / IleRS


Mass: 105090.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gram-positive bacterium / Source: (gene. exp.) Priestia megaterium (bacteria) / Strain: DSM-32 / Cell: bacterial / Gene: ileS, BG04_1180 / Plasmid: pET28b(+) / Details (production host): Kan(R) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B6A6A8, isoleucine-tRNA ligase

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Non-polymers , 6 types, 18 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ILA / N-[ISOLEUCINYL]-N'-[ADENOSYL]-DIAMINOSUFONE


Mass: 458.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N8O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na

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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: 3.62 Å3/Da / Density % sol: 66.03 %
Description: Single bipyramidal crystals. Susceptible to cracking upon temperature change.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5 mM Ile-AMS and 20 mg/ml wt-HMGH-PmIleRS1 were mixed in 1:1 ratio with the well solution containing: 300 mM lithium sulfate, 150 mM sodium sulfate, and 15 - 25 % PEG3350, 25 mM Hepes-KOH ...Details: 5 mM Ile-AMS and 20 mg/ml wt-HMGH-PmIleRS1 were mixed in 1:1 ratio with the well solution containing: 300 mM lithium sulfate, 150 mM sodium sulfate, and 15 - 25 % PEG3350, 25 mM Hepes-KOH pH=7.5 at 20 oC, 50 mM NaCl. The drop volume of 2 microliters, was equilibrated towards 300 microliters of the well solution at 19 degrees.
PH range: 6.8-8.2
Temp details: Susceptible to cracking upon temperature change.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0000305674359 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0000305674359 Å / Relative weight: 1
ReflectionResolution: 2.9→48.77 Å / Num. obs: 34322 / % possible obs: 92.86 % / Redundancy: 20.8 % / Biso Wilson estimate: 110.52 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06695 / Rpim(I) all: 0.01511 / Rrim(I) all: 0.06867 / Net I/σ(I): 30.66
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 22 % / Rmerge(I) obs: 3.219 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 2499 / CC1/2: 0.605 / CC star: 0.868 / Rpim(I) all: 0.7003 / Rrim(I) all: 3.295 / % possible all: 74.11

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20190806data reduction
XSCALE20190806data scaling
PHASERCCP4Interface 7.0.077phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.77 Å / SU ML: 0.488 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 33.4581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2692 1827 5.73 %
Rwork0.2424 30063 -
obs0.244 31890 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 155.16 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7401 0 106 0 7507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00177680
X-RAY DIFFRACTIONf_angle_d0.424910431
X-RAY DIFFRACTIONf_chiral_restr0.04021128
X-RAY DIFFRACTIONf_plane_restr0.00341335
X-RAY DIFFRACTIONf_dihedral_angle_d10.01882819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.980.42321110.39951772X-RAY DIFFRACTION72.9
2.98-3.070.41291130.36811968X-RAY DIFFRACTION79.85
3.07-3.160.37161330.36012043X-RAY DIFFRACTION83.5
3.17-3.280.31191330.32982221X-RAY DIFFRACTION89.3
3.28-3.410.33531370.32792240X-RAY DIFFRACTION92.31
3.41-3.560.34031410.31512350X-RAY DIFFRACTION95.19
3.56-3.750.31471470.27562411X-RAY DIFFRACTION96.97
3.75-3.990.30581490.26562442X-RAY DIFFRACTION98.26
3.99-4.290.28031480.252450X-RAY DIFFRACTION99.08
4.3-4.730.2411490.22072494X-RAY DIFFRACTION99.44
4.73-5.410.25771450.22692492X-RAY DIFFRACTION99.81
5.41-6.810.30251540.26152536X-RAY DIFFRACTION99.93
6.81-48.770.21611670.19222644X-RAY DIFFRACTION99.93
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)
10.4493903142990.276883441560.2772966694160.317962172503-0.3387961906571.750331349780.188905272666-0.228915320975-0.3128710070030.853876456378-0.514166997284-1.087459252790.482923251235-0.227968331734-0.1710462663430.8901564921790.0192116092911-0.4169762296240.7485762436920.1461140133381.34646598125-46.5745405902-23.3371449127-8.94001551891
21.440437283710.238399311647-0.8684939533981.81724479397-0.251474779620.9871720186360.1794084695370.3550169033070.074833664982-0.635284066554-0.09367342350390.251013553290.232547087969-0.266036680251.93127439818E-50.8741903172590.107137023872-0.1485577036731.16936142229-0.04677530032090.632362821247-83.709384874-24.1473384787-40.0433694935
31.38589959026-0.00567244969747-0.2377683525861.50502303590.3315140400810.7162773051590.0741262611847-0.2408948170430.1732126515920.909720618334-0.0604260855150.104129383739-0.0206385718913-0.25441926337-1.87676684395E-51.02098503504-0.0246936063685-0.03313673118111.01993397170.005369244896760.711247474129-69.7949349143-23.8900341008-7.07481510264
40.2009493554710.26028410560.1400606925030.2976155989490.335728495590.8079564471320.0229814205217-0.5150663331980.07221099346310.769566059641-0.157540772769-1.29278522893-0.1229543934050.560158334016-0.8191689165650.706154405301-0.31111955594-1.112432848751.100596242860.2999797393532.72988697576-25.18918507932.92145899556-8.79674027461
50.114311724605-0.0906894660897-0.1898064747330.507200208377-0.4087125756370.8848446171010.4523932462410.5343956383350.6814593040590.4567342762360.0504565693166-0.913304219039-0.8732647419060.4860453255970.01028987111061.01208020298-0.128421960887-0.390188753961.639028491740.420223027242.50649529249-17.816602991423.7510797915-23.5500301119
60.0829554099855-0.03185499961280.003899189979720.0322565714128-0.01217863768130.01462813510890.1182210700310.1690794934830.432227440930.532730041017-0.457050756168-0.1482243859680.201841709095-0.182287231875-2.12223821119E-61.98835463182-0.274668927036-0.7539158304311.910189007320.3643499646573.952592269962.4665992118415.0404302458-10.1941474514
71.11854967322-0.808615427435-1.376340821520.6752013834591.25171392722.444372989950.05801142609120.7571415099370.175177021784-0.627251346846-0.178366840595-1.15943117544-0.608431260962-0.376365337843-0.05820988579820.761284143774-0.1559262500090.03202914546880.712537003310.2111534074381.56228915852-41.9612101419-14.3527070113-25.30136388
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 20 through 155)20 - 15520 - 155
22chain 'A' and (resid 181 through 409 )181 - 409181 - 409
33chain 'A' and ((resid 410 through 584 ) or (resid 156 through 180))156 - 584156 - 584
44chain 'A' and ((resid 633 through 791 ) or (resid 1 through 19))1 - 7911 - 791
55chain 'A' and (resid 792 through 881 )792 - 881792 - 881
66chain 'A' and (resid 882 through 921 )882 - 921882 - 921
77chain 'A' and (resid 585 through 632 )585 - 632585 - 632

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