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- PDB-8qij: Crystallographic Structure of a Salicylate Synthase from M. absce... -

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Basic information

Entry
Database: PDB / ID: 8qij
TitleCrystallographic Structure of a Salicylate Synthase from M. abscessus (Mab-SaS)
ComponentsPutative anthranilate synthase component I TrpE2/ Salicylate synthase MbtI
KeywordsBIOSYNTHETIC PROTEIN / Synthase / Siderophore / Iron Acquisition
Function / homology
Function and homology information


oxo-acid-lyase activity / isochorismate synthase activity / biosynthetic process / metal ion binding
Similarity search - Function
Salicylate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Anthranilate synthase component I TrpE2/ Salicylate synthase MbtI
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.073 Å
AuthorsCassetta, A. / Covaceuszach, S. / Tomaiuolo, M. / Meneghetti, F. / Villa, S. / Mori, M. / Chiarelli, L.R. / Mangiatordi, G.F.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione Ricerca Fibrosi CisticaFFC#5/2022 Italy
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Structural basis for specific inhibition of salicylate synthase from Mycobacterium abscessus.
Authors: Mori, M. / Cocorullo, M. / Tresoldi, A. / Cazzaniga, G. / Gelain, A. / Stelitano, G. / Chiarelli, L.R. / Tomaiuolo, M. / Delre, P. / Mangiatordi, G.F. / Garofalo, M. / Cassetta, A. / ...Authors: Mori, M. / Cocorullo, M. / Tresoldi, A. / Cazzaniga, G. / Gelain, A. / Stelitano, G. / Chiarelli, L.R. / Tomaiuolo, M. / Delre, P. / Mangiatordi, G.F. / Garofalo, M. / Cassetta, A. / Covaceuszach, S. / Villa, S. / Meneghetti, F.
History
DepositionSep 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.entity_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative anthranilate synthase component I TrpE2/ Salicylate synthase MbtI
C: Putative anthranilate synthase component I TrpE2/ Salicylate synthase MbtI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,20818
Polymers97,6212
Non-polymers1,58716
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-136 kcal/mol
Surface area32030 Å2
Unit cell
Length a, b, c (Å)94.340, 94.760, 102.460
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 AC

#1: Protein Putative anthranilate synthase component I TrpE2/ Salicylate synthase MbtI


Mass: 48810.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 1-15 and 453 are missing in the crystallographic model due to the lack of electron density.
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: MAB_2245 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MAQ5

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Non-polymers , 5 types, 359 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.41 % / Description: Thin rods
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23-27% PEG 3350, 0.15-0.25M ammonium sulphate, 0.1M BIS-TRIS (pH 5.5)
PH range: 5.4-5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2022 / Details: Pt-coated cylindrical mirror
RadiationMonochromator: Double Crystal Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→56.1 Å / Num. obs: 56395 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.057 / Rrim(I) all: 0.195 / Net I/σ(I): 11.9
Reflection shellResolution: 2.073→2.109 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.281 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2794 / CC1/2: 0.818 / Rpim(I) all: 0.389 / Rrim(I) all: 1.34 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROC1.0.5 (20220608)data reduction
autoPROC1.0.5 (20220608)data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.073→56.054 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.283 / SU ML: 0.136 / SU R Cruickshank DPI: 0.1967 / Cross valid method: FREE R-VALUE / ESU R: 0.197 / ESU R Free: 0.166 / SU Rfree Cruickshank DPI: 0.166
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2171 2677 4.747 %
Rwork0.1769 53717 -
all0.179 --
obs-56394 99.963 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.933 Å20 Å2-0 Å2
2---2.589 Å20 Å2
3---0.656 Å2
Refinement stepCycle: LAST / Resolution: 2.073→56.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 91 343 7070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0126851
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166400
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.6519316
X-RAY DIFFRACTIONr_angle_other_deg0.4091.57214709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9285872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.81572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.157101061
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.34810311
X-RAY DIFFRACTIONr_chiral_restr0.0570.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021553
X-RAY DIFFRACTIONr_nbd_refined0.2010.21351
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.25846
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23320
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23709
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2412
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1490.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1040.210
X-RAY DIFFRACTIONr_nbd_other0.140.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.210
X-RAY DIFFRACTIONr_mcbond_it2.2263.2823490
X-RAY DIFFRACTIONr_mcbond_other2.2233.2813489
X-RAY DIFFRACTIONr_mcangle_it3.4785.8874357
X-RAY DIFFRACTIONr_mcangle_other3.4815.8894358
X-RAY DIFFRACTIONr_scbond_it2.9693.7173361
X-RAY DIFFRACTIONr_scbond_other2.9363.6973322
X-RAY DIFFRACTIONr_scangle_it4.7586.6554958
X-RAY DIFFRACTIONr_scangle_other4.7216.6184899
X-RAY DIFFRACTIONr_lrange_it6.58532.9617711
X-RAY DIFFRACTIONr_lrange_other6.5432.8817632
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.073-2.1270.2661860.25639140.25641030.9430.94899.92690.239
2.127-2.1850.2822080.23538330.23740420.9330.95799.97530.215
2.185-2.2480.2621830.22137130.22338970.9520.96399.97430.199
2.248-2.3170.2461850.21335880.21537730.9590.9681000.189
2.317-2.3930.2641780.20434920.20736700.9540.9711000.179
2.393-2.4770.2511840.19834050.20135900.9650.97499.97210.17
2.477-2.570.251570.18132680.18434250.9620.981000.155
2.57-2.6750.2281580.18831750.1933330.9680.9781000.161
2.675-2.7930.2251200.17630680.17831890.9670.98299.96860.15
2.793-2.9290.2481360.18828950.19130320.9650.97999.9670.162
2.929-3.0870.2361530.18627610.18929140.9640.9791000.163
3.087-3.2740.2481180.17926430.18127610.9590.981000.162
3.274-3.4990.2231400.17424740.17726140.9710.9831000.161
3.499-3.7780.2281130.16523200.16824330.9740.9851000.156
3.778-4.1370.187860.14921490.1522360.9780.98799.95530.144
4.137-4.6220.1531190.12719190.12920380.9870.9911000.13
4.622-5.3310.1711220.14716990.14818220.9820.98999.94510.151
5.331-6.5150.198570.19514980.19515550.9770.9831000.195
6.515-9.1510.198480.14211830.14412320.9820.98999.91880.151
9.151-56.0540.115260.177200.1687530.990.98399.07040.189

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