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- PDB-8c9f: Priestia megaterium inactive HIGH motif mutant of type1 isoleucyl... -

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Basic information

Entry
Database: PDB / ID: 8c9f
TitlePriestia megaterium inactive HIGH motif mutant of type1 isoleucyl-tRNA synthetase 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: 3.1 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)106,99321
Polymers105,0911
Non-polymers1,90220
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 area3740 Å2
ΔGint-156 kcal/mol
Surface area40290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.040, 127.040, 163.380
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 / Mutation: H64G, G66H
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 / Variant: de Bary 1884 / Plasmid: pET28b(+) / Details (production host): EMD Biosciences, Cat: 69865-3 / Cell (production host): bacterial / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / Variant (production host): BL21(DE3) / References: UniProt: A0A0B6A6A8, isoleucine-tRNA ligase

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Non-polymers , 6 types, 20 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.: 2 / Source method: obtained synthetically / Formula: Li
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / 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: 66.04 %
Description: Single tetragonal 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 mut-GMHH-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 mut-GMHH-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 4 degrees.
PH range: 6.8-8.2
Temp details: Crystal suscteptible to breaking 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: 3.1→48.81 Å / Num. obs: 28199 / % possible obs: 90.83 % / Redundancy: 20.7 % / Biso Wilson estimate: 110.31 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1224 / Rpim(I) all: 0.02748 / Rrim(I) all: 0.1255 / Net I/σ(I): 19.7
Reflection shellResolution: 3.1→3.211 Å / Redundancy: 21.8 % / Rmerge(I) obs: 3.731 / Mean I/σ(I) obs: 1 / Num. unique obs: 1927 / CC1/2: 0.586 / CC star: 0.859 / Rpim(I) all: 0.8137 / Rrim(I) all: 3.82 / % possible all: 90.83

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20190806data reduction
XSCALE20190806data scaling
PHASERCCP4Interface 7.0.077phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.81 Å / SU ML: 0.4745 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 33.0033
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2763 1830 7.14 %
Rwork0.2391 23800 -
obs0.2418 25630 90.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 153.23 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7401 0 108 0 7509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00197680
X-RAY DIFFRACTIONf_angle_d0.429810431
X-RAY DIFFRACTIONf_chiral_restr0.04031128
X-RAY DIFFRACTIONf_plane_restr0.00341335
X-RAY DIFFRACTIONf_dihedral_angle_d11.90982819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.43011150.38881363X-RAY DIFFRACTION68.84
3.18-3.280.41061090.36821484X-RAY DIFFRACTION74.72
3.28-3.380.44961240.35471596X-RAY DIFFRACTION81.25
3.38-3.50.36251320.31911703X-RAY DIFFRACTION85.47
3.5-3.640.32871420.29591797X-RAY DIFFRACTION90.02
3.64-3.810.32251430.26841869X-RAY DIFFRACTION93.71
3.81-4.010.29361450.26631890X-RAY DIFFRACTION94.56
4.01-4.260.24791420.24881934X-RAY DIFFRACTION96.51
4.26-4.590.23951540.21561965X-RAY DIFFRACTION97.47
4.59-5.050.28911530.22081994X-RAY DIFFRACTION98.89
5.05-5.780.24521590.24732017X-RAY DIFFRACTION99.41
5.78-7.280.32031590.26022032X-RAY DIFFRACTION99.46
7.28-48.810.22131530.18722156X-RAY DIFFRACTION99.53
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)
10.6098290775930.0962201489943-0.1286052697530.4382258235010.6520346305992.05469568082-0.262576599856-0.306031069835-0.1374165158650.791597529425-0.410531365863-0.9714815725480.319937859311-0.0829692863382-0.8225317565380.4527980397920.0112561518048-0.5944644522220.5166476562660.1512240681571.01356179373-46.4850151665-23.3132007737-8.86233066393
20.66886076077-0.0185802039301-0.4270156142320.8572953704070.07978654277590.2972833481010.09526175215060.557080046507-0.115861807883-0.758924552822-0.09011633532870.2255833560920.154100516352-0.0180149345255-1.6793594302E-51.024840603840.075636263972-0.1800776385981.26272225723-0.03763919278150.721245768606-83.6458262399-24.1827172347-39.9227183301
30.947380927719-0.111806071972-0.1131607380180.6563735384720.1326512319520.30227780502-0.021725815087-0.3350485894360.09600144239460.789456040329-0.0530106975664-0.0598830966425-0.0734826006-0.245808130946-1.82161721769E-50.892679945525-0.0519102646056-0.03722217688130.912016513574-0.046304402330.575496009821-69.6748311049-23.8559965506-6.97272043384
40.6060431524620.2384479479290.06265308874010.5122334399760.1741081327981.30231971165-0.0536974603879-0.4340784747230.1057547980260.581603739174-0.144141043386-1.43647458132-0.1088786180350.569925257872-0.9032459085470.708557793169-0.323641297068-1.079093229060.7684584098510.1445569552752.52919955914-25.10089431832.93801810546-8.79446261321
50.0055490658681-0.0340315800677-0.004718651541070.117815152422-0.06346237231720.03451412785550.2456190266220.6366195542560.1038900906640.0872534861030.201352734339-0.691037169003-0.5277172009730.7308012214450.000329631730291.31810673202-0.0897304568262-0.4048552017921.647811383380.2897192923472.41529562771-17.76491454423.7473736763-23.5667461742
60.006788463009610.0182167651139-0.00539599685990.0193732396058-0.006182202668390.006320936333690.0468232578455-0.07739039186560.5421015800410.373307307044-0.187725239985-0.4018236439240.02905194264540.0321147728295-8.29541027176E-51.52942655809-0.411576933006-0.5859102718731.522811858490.424999668462.778751345732.5537433163815.0672714821-10.2297230612
70.0346250852874-0.0250429415698-0.04317161065290.105925856385-0.07506733455340.1158021053120.2497475540410.342518610867-0.0317935357644-0.6960376899-0.30702749602-0.395352385222-0.302599637859-0.2944760194146.6286501191E-50.745050607884-0.00311978989848-0.07106848222540.7853003572470.07182452278211.19519471465-41.869215387-14.3398537422-25.3017163694
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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