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- PDB-8qc4: M. tuberculosis salicylate synthase MbtI in complex with 5-(3-car... -

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Basic information

Entry
Database: PDB / ID: 8qc4
TitleM. tuberculosis salicylate synthase MbtI in complex with 5-(3-carboxyphenyl)furan-2-carboxylic acid
ComponentsSalicylate synthase
KeywordsLYASE / salicylate / isochorismate / chorismate / mycobactins
Function / homology
Function and homology information


isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity ...isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity / response to host immune response / tryptophan biosynthetic process / magnesium ion binding / plasma membrane
Similarity search - Function
Salicylate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme
Similarity search - Domain/homology
5-(3-carboxyphenyl)furan-2-carboxylic acid / Salicylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.578 Å
AuthorsMori, M. / Villa, S. / Meneghetti, F. / Bellinzoni, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
University and Research - University of Milan Italy
CitationJournal: Pharmaceuticals / Year: 2023
Title: Structural Study of a New MbtI-Inhibitor Complex: Towards an Optimized Model for Structure-Based Drug Discovery.
Authors: Mori, M. / Villa, S. / Chiarelli, L.R. / Meneghetti, F. / Bellinzoni, M.
History
DepositionAug 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Other / Category: citation / pdbx_database_status
Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Salicylate synthase
B: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8399
Polymers97,8992
Non-polymers9417
Water15,259847
1
A: Salicylate synthase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 49.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)49,3704
Polymers48,9491
Non-polymers4203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Salicylate synthase
hetero molecules


  • defined by author
  • 49.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)49,4705
Polymers48,9491
Non-polymers5204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.092, 84.001, 93.683
Angle α, β, γ (deg.)90, 110.53, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Salicylate synthase /


Mass: 48949.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: mbtI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFX1
#2: Chemical ChemComp-TXR / 5-(3-carboxyphenyl)furan-2-carboxylic acid


Mass: 232.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H8O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 8000, 0.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.578→87.735 Å / Num. obs: 93645 / % possible obs: 94.6 % / Redundancy: 6.85 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.998 / CC1/2 anomalous: -0.252 / Rmerge(I) obs: 0.0746 / Rpim(I) all: 0.0309 / Rrim(I) all: 0.0808 / AbsDiff over sigma anomalous: 0.728 / Baniso tensor eigenvalue 1: 22.4468 Å2 / Baniso tensor eigenvalue 2: 3.1367 Å2 / Baniso tensor eigenvalue 3: 0 Å2 / Baniso tensor eigenvector 1 ortho1: 0.9595 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: -0.2818 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0.2818 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.9595 / Aniso diffraction limit 1: 2.093 Å / Aniso diffraction limit 2: 1.635 Å / Aniso diffraction limit 3: 1.578 Å / Aniso diffraction limit axis 1 ortho1: 0.9571 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: -0.28957 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0.28957 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.9571 / Net I/σ(I): 12.71 / Num. measured all: 641863 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 94.4 / % possible ellipsoidal: 94.6 / % possible ellipsoidal anomalous: 94.4 / % possible spherical: 69.1 / % possible spherical anomalous: 68.9 / Redundancy anomalous: 3.48 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
4.887-87.7356.860.034139.323210732107468246820.998-0.3740.01410.0370.57399.999.899.999.899.93.5899.8
3.871-4.8876.40.038436.322996529965468246820.998-0.3010.01630.04180.69299.899.899.899.899.83.2999.8
3.376-3.8716.750.047131.283161431614468346830.997-0.2020.01960.05110.75799.910099.910099.93.45100
3.065-3.3766.350.055425.972971429714468146810.997-0.1770.0240.06050.77599.699.899.699.899.63.2399.8
2.843-3.0656.90.072221.323232132321468346830.996-0.2260.02980.07820.7591001001001001003.51100
2.675-2.8437.060.089817.483304733047468346830.995-0.1720.03650.0970.7551001001001001003.59100
2.539-2.6757.160.112914.443351033510468146810.993-0.1220.04550.12180.7481001001001001003.63100
2.428-2.5397.230.139312.023383133831468246820.992-0.0830.05590.15020.7599.910099.910099.93.67100
2.334-2.4287.260.166910.333399533995468346830.99-0.0720.06660.17980.74299.910099.910099.93.68100
2.253-2.3346.750.24077.463159931599468346830.981-0.0890.10010.2610.74499.810099.810099.83.42100
2.182-2.2536.610.30136.313094130941468146810.966-0.0780.12690.32750.76299.799.899.799.899.73.3599.8
2.119-2.1826.980.29666.263270232702468446840.9740.0070.12040.32050.73498.398.298.398.298.33.5398.2
2.059-2.1197.020.33185.743287832878468246820.967-0.0510.13440.35840.72595.795.695.794.494.73.5595.6
2.003-2.0597.070.39464.893312133121468246820.952-0.0080.15910.42590.73896.296.296.289.589.93.5796.2
1.948-2.0036.770.47763.953169531695468246820.929-0.0430.19710.51740.7294.494.694.480.981.13.4294.6
1.893-1.9486.570.72592.653076430764468346830.833-0.0490.30470.78870.75191.591.891.571.771.83.3291.8
1.837-1.8936.780.66782.713173431734468146810.843-0.0330.27490.72330.70690.490.990.463.863.83.4390.9
1.781-1.8376.780.77662.293176031760468146810.784-0.0010.32040.84150.7139191.49156.156.23.4391.4
1.72-1.7816.850.92981.913206132061468346830.715-0.0270.38271.00710.70287.587.887.545.245.43.4587.8
1.578-1.726.941.11151.553250432504468346830.6250.020.45381.2020.71363.363.863.315.215.23.5263.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5 20220608data processing
autoPROC1.0.5 20220608data reduction
PHASERphasing
Aimlessdata scaling
autoPROC1.0.5 20220608data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.578→22.76 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 4717 -RANDOM
Rwork0.1787 ---
obs0.18 93600 69 %-
Displacement parametersBiso mean: 31.21 Å2
Baniso -1Baniso -2Baniso -3
1-3.2165 Å20 Å2-1.4049 Å2
2---1.5816 Å20 Å2
3----1.6349 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.578→22.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6671 0 60 847 7578
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016853HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.969307HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2386SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1201HARMONIC5
X-RAY DIFFRACTIONt_it6853HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion888SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6933SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.96
X-RAY DIFFRACTIONt_other_torsion13.88
LS refinement shellResolution: 1.58→1.67 Å
RfactorNum. reflection% reflection
Rfree0.2885 92 -
Rwork0.2633 --
obs0.2645 1872 8.91 %
Refinement TLS params.

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)
117.3209-0.8986-8.81259.2259-2.514411.11610.5284-0.0742-0.6529-0.0742-0.1522-0.1004-0.6529-0.1004-0.37610.22230.0259-0.0232-0.1479-0.0369-0.0906-29.733320.4463-6.3443
20.64890.6777-0.17673.00650.21661.6140.0310.31960.07270.3196-0.016-0.05420.0727-0.0542-0.0149-0.01990.006-0.0244-0.1114-0.0019-0.1147-27.1541-3.6405-5.4103
38.1764-2.18420.967135.61441.45645.2887-0.00291.4622-0.10831.46220.3247-0.3392-0.1083-0.3392-0.32170.0543-0.00180.011-0.0330.0386-0.0705-39.411-7.2805-5.0952
40.9098-0.5724-0.29142.44651.34532.2191-0.02720.11450.05760.1145-0.0049-0.05990.0576-0.05990.0321-0.0586-0.0068-0.0144-0.13050.0147-0.1233-27.8397-3.1484-9.1727
50.5996-0.246-0.33711.13170.15621.6842-0.0035-0.02380.034-0.0238-0.01140.30110.0340.30110.0149-0.0502-0.0011-0.0255-0.07560.0096-0.077-11.74360.4332-18.2559
60.92410.2752-0.53661.0617-0.26722.02580.006-0.06260.0039-0.06260.061-0.23170.0039-0.2317-0.0671-0.0117-0.0057-0.034-0.05770.0131-0.0918-27.71430.2838-32.7201
71.0528-0.0453-0.27030.8223-0.11341.47090.0035-0.09180.1738-0.0918-0.03260.0460.17380.0460.0291-0.00120.0117-0.0113-0.1274-0.0026-0.1262-19.9453-8.9064-22.1571
82.0066-0.9671-1.03757.08736.21699.00130.0345-0.3509-0.0219-0.3509-0.00260.3628-0.02190.3628-0.0319-0.0293-0.026-0.0001-0.03920.0497-0.0389-6.66461.1656-24.934
9-0.622-12.62277.13688.8657-7.30635.45880.3373-1.2560.2411-1.256-0.15160.56530.24110.5653-0.18580.0160.019-0.0730.00670.0127-0.0406-16.5616-3.9304-29.7555
101.7349-0.07991.17131.83310.82121.90620.0399-0.01390.0177-0.0139-0.0589-0.35460.0177-0.35460.019-0.02410.0043-0.0146-0.01910.0113-0.0723-23.47195.552520.4125
112.3560.42920.63121.5540.45741.8723-0.0087-0.0824-0.2572-0.0824-0.0429-0.2396-0.2572-0.23960.05170.01360.0224-0.0217-0.06910.0093-0.1042-15.57913.979624.8642
1212.78184.3314-0.49866.46820.17597.74090.0093-0.94130.3217-0.9413-0.073-1.51670.3217-1.51670.06380.0205-0.28270.08450.898-0.44660.5057-36.4328-1.208516.4154
133.82571.71681.9322.43270.84232.39620.2509-0.15050.1621-0.1505-0.03910.44380.16210.4438-0.21180.00770.0757-0.0293-0.0244-0.026-0.00292.6909-3.299717.2825
141.4963-0.3491.11661.00470.34532.23190.15620.02150.20790.02150.028-0.090.2079-0.09-0.1842-0.0249-0.0077-0.0458-0.10090.0171-0.069-11.1509-2.7323.9501
153.5772-3.67560.91648.99530.47762.46560.1961-0.3590.1567-0.359-0.10110.09820.15670.0982-0.09490.0370.03-0.0492-0.0219-0.0061-0.04554.0777-7.534537.1197
162.9111-1.39941.0732.9212-0.27313.0483-0.13310.4161-0.02650.41610.2955-0.2046-0.0265-0.2046-0.1624-0.00330.0145-0.0240.03240.0269-0.0984-5.40712.277341.4769
171.44310.09740.96471.223-0.00331.85930.1493-0.06630.0401-0.0663-0.03290.16050.04010.1605-0.1165-0.03960.0077-0.0327-0.08530.0104-0.063-1.28282.281122.7219
184.7642.1299-8.99779.4624-10.269714.079-0.14980.5128-0.13640.5128-0.5041.5109-0.13641.51090.65380.0610.0042-0.03840.08870.0601-0.0022.4684-2.495826.9403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|13 - 25}A13 - 25
2X-RAY DIFFRACTION2{A|26 - 93}A26 - 93
3X-RAY DIFFRACTION3{A|94 - 103}A94 - 103
4X-RAY DIFFRACTION4{A|104 - 160}A104 - 160
5X-RAY DIFFRACTION5{A|161 - 248}A161 - 248
6X-RAY DIFFRACTION6{A|249 - 350}A249 - 350
7X-RAY DIFFRACTION7{A|351 - 426}A351 - 426
8X-RAY DIFFRACTION8{A|427 - 450}A427 - 450
9X-RAY DIFFRACTION9{A|501}A501
10X-RAY DIFFRACTION10{B|15 - 80}B15 - 80
11X-RAY DIFFRACTION11{B|81 - 155}B81 - 155
12X-RAY DIFFRACTION12{B|156 - 164}B156 - 164
13X-RAY DIFFRACTION13{B|165 - 211}B165 - 211
14X-RAY DIFFRACTION14{B|212 - 274}B212 - 274
15X-RAY DIFFRACTION15{B|275 - 310}B275 - 310
16X-RAY DIFFRACTION16{B|311 - 348}B311 - 348
17X-RAY DIFFRACTION17{B|349 - 449}B349 - 449
18X-RAY DIFFRACTION18{B|501}B501

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