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- PDB-7pd2: Crystal structure of the substrate-free radical SAM tyrosine lyas... -

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Basic information

Entry
Database: PDB / ID: 7pd2
TitleCrystal structure of the substrate-free radical SAM tyrosine lyase ThiH (2-iminoacetate synthase) from Thermosinus carboxydivorans
ComponentsThiazole biosynthesis protein ThiH
KeywordsLYASE / Radical SAM enzyme 2-iminoacetate Metalloprotein
Function / homology
Function and homology information


thiamine biosynthetic process / catalytic activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Thiazole biosynthesis ThiH / ThiH/NocL/HydG-like / Biotin and Thiamin Synthesis associated domain / Biotin and thiamin synthesis-associated domain / Biotin and Thiamin Synthesis associated domain / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
5'-DEOXYADENOSINE / METHIONINE / IRON/SULFUR CLUSTER / Thiazole biosynthesis protein ThiH
Similarity search - Component
Biological speciesThermosinus carboxydivorans Nor1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsAmara, P. / Saragaglia, C. / Mouesca, J.-M. / Martin, L. / Nicolet, Y.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE29-0019 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-05-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
CitationJournal: Nat Commun / Year: 2022
Title: L-tyrosine-bound ThiH structure reveals C-C bond break differences within radical SAM aromatic amino acid lyases.
Authors: Amara, P. / Saragaglia, C. / Mouesca, J.M. / Martin, L. / Nicolet, Y.
History
DepositionAug 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiazole biosynthesis protein ThiH
B: Thiazole biosynthesis protein ThiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,42717
Polymers86,0702
Non-polymers2,35715
Water4,450247
1
A: Thiazole biosynthesis protein ThiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2609
Polymers43,0351
Non-polymers1,2248
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiazole biosynthesis protein ThiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1678
Polymers43,0351
Non-polymers1,1327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.090, 49.330, 85.210
Angle α, β, γ (deg.)90.000, 96.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-616-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thiazole biosynthesis protein ThiH / 2-iminoacetate synthase ThiH


Mass: 43035.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosinus carboxydivorans Nor1 (bacteria)
Gene: TcarDRAFT_1903 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1HPQ5

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Non-polymers , 6 types, 262 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.4-1.6 M (NH4)2SO4, 100 mM MES buffer pH 6.5, 15% dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→47.46 Å / Num. obs: 94609 / % possible obs: 97 % / Redundancy: 6.1 % / Rsym value: 0.21 / Net I/σ(I): 6.11
Reflection shellResolution: 1.99→2.04 Å / Num. unique obs: 6300 / CC1/2: 0.23

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PD1

7pd1


Resolution: 1.99→47.46 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 31.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 4725 4.99 %
Rwork0.2298 89884 -
obs0.2318 94609 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.64 Å2 / Biso mean: 43.4907 Å2 / Biso min: 24.65 Å2
Refinement stepCycle: final / Resolution: 1.99→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 0 118 247 6145
Biso mean--52.92 44.6 -
Num. residues----732
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.010.40561510.45322822297392
2.01-2.040.41511530.37142959311296
2.04-2.060.34441580.36042992315097
2.06-2.090.37091540.33382921307597
2.09-2.120.3391590.33332999315897
2.12-2.140.3991570.32212964312197
2.14-2.170.35021540.31722964311897
2.17-2.210.3351570.31352998315597
2.21-2.240.30291570.30632996315397
2.24-2.280.33321580.30972956311498
2.28-2.320.36011540.30452970312497
2.32-2.360.32321600.28683035319597
2.36-2.410.34251570.28823002315998
2.41-2.450.34771540.27922989314397
2.45-2.510.27411530.28282964311797
2.51-2.570.38661560.27492991314798
2.57-2.630.34371590.27793010316998
2.63-2.70.31091590.26142997315698
2.7-2.780.29591600.25423027318798
2.78-2.870.32021640.24443028319298
2.87-2.970.30731540.23282994314898
2.97-3.090.28611610.23383053321499
3.09-3.230.26921600.22993012317298
3.23-3.40.25411550.2072992314798
3.4-3.620.20331580.19523030318898
3.62-3.90.26291590.19173056321599
3.9-4.290.20191610.17993014317599
4.29-4.910.20931620.17363066322899
4.91-6.180.23841610.19453038319999
6.18-47.460.21621600.19743045320599
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)
10.5069-0.12370.40471.0435-0.40951.63530.06510.28420.3397-0.04930.13720.288-0.0192-0.4309-0.09640.3538-0.056-0.01610.5085-0.02810.3484-19.079-5.02719.695
21.58221.03910.70142.76650.73882.5165-0.2456-0.11340.22430.0750.19940.17320.0244-0.14320.06840.34910.038-0.03930.37930.01480.3273-13.6134.74717.428
30.5216-0.4589-0.57611.1233-0.00562.8727-0.27-0.2102-0.16460.01520.30440.15380.1219-0.5390.07740.31220.0061-0.04330.3823-0.01550.3753-24.943-1.6267.651
44.2675-0.90140.20433.2615-0.03182.1645-0.02860.08480.0541-0.3732-0.02530.0693-0.21470.45560.01570.4002-0.02020.00890.3372-0.0180.2473-15.1146.449-0.365
52.86871.6552.6691.90971.30333.7382-1.3532-1.04481.54991.0829-0.2566-1.19040.2631-1.6541.56890.49020.2224-0.08540.5402-0.00140.4724-18.483-15.91614.7
63.1443-1.76051.03633.6392-2.02693.6603-0.3327-0.82380.01011.05990.28750.069-0.79220.54010.05670.5143-0.0338-0.0170.3908-0.02150.350121.6915.84953.046
71.10031.2260.03531.4908-0.00553.27840.0538-0.1369-0.41840.18960.0459-0.10770.55220.0878-0.03140.35560.07370.00240.3845-0.02690.398519.414-12.4442.827
81.44130.11820.11520.66850.06161.6349-0.0745-0.16890.3633-0.13960.00160.1857-0.2559-0.050.04420.3597-0.0071-0.01170.3695-0.03030.363624.10216.61321.027
91.48050.8550.09052.3851-0.38582.20570.3192-0.3864-0.00340.0697-0.15210.0733-0.07950.128-0.06250.3124-0.0240.0380.2774-0.06640.357821.16315.02936.932
100.44070.663-0.70391.6073-0.41431.66340.0256-0.1102-0.05130.10090.0621-0.1011-0.05440.3955-0.08380.31270.028-0.04110.4023-0.03310.338324.3631.53336.886
111.7964-0.0650.53232.95420.36262.34390.07250.18150.0598-0.0346-0.0771-0.2307-0.01580.64540.07890.34550.0097-0.0220.5108-0.02650.306230.5852.24621.177
124.339-0.9317-0.74893.9185-0.68553.36620.0445-0.8599-0.1434-0.01860.29580.43320.1805-0.0197-0.31590.3937-0.0452-0.01780.36250.01350.31817.931-5.72617.131
1326.8127-9.44948.1446-7.65042-1.27970.5905-1.02661.4413-1.41661.50570.5048-1.2082.6430.47990.0919-0.03280.3078-0.15011.031927.0616.67230.119
140.8754-1.2787-0.24632.86361.55192.6563-0.0224-0.2363-0.21280.3936-0.176-0.07970.1350.06550.16270.45620.0475-0.07590.70150.05850.3488-5.457-4.57834.355
151.48070.03650.12291.6414-0.5583.5413-0.0885-0.35310.3350.29810.0569-0.3358-0.45990.4222-0.00030.4227-0.0267-0.02850.4806-0.07710.4351-6.66813.11723.979
160.9558-0.2042-0.08191.26460.12382.0731-0.07540.137-0.2154-0.3140.06430.15690.3807-0.06550.00230.31260.0191-0.01350.29870.00930.2873-23.009-14.2826.628
172.87480.2712-0.26082.2435-0.05922.8378-0.0241-0.0048-0.2388-0.2282-0.14950.15320.11320.25240.07980.3569-0.0217-0.05620.38080.02920.3723-14.307-17.6823.579
182.45260.1745-0.20561.42030.18532.01020.0577-0.3794-0.18780.1566-0.0729-0.08220.08330.12970.00850.34840.015-0.02370.41810.06530.3139-10.414-14.19818.807
193.0701-1.18460.01441.58650.59171.9984-0.1343-0.7698-0.44050.3170.0118-0.11540.30030.20530.01610.3539-0.0091-0.00980.4890.00660.399-6.252-3.07524.078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 249:275 )B249 - 275
2X-RAY DIFFRACTION2( CHAIN B AND RESID 276:302 )B276 - 302
3X-RAY DIFFRACTION3( CHAIN B AND RESID 303:344 )B303 - 344
4X-RAY DIFFRACTION4( CHAIN B AND RESID 345:366 )B345 - 366
5X-RAY DIFFRACTION5( CHAIN B AND RESID 403:403 )B403
6X-RAY DIFFRACTION6( CHAIN A AND RESID 1:22 )A1 - 22
7X-RAY DIFFRACTION7( CHAIN A AND RESID 23:69 )A23 - 69
8X-RAY DIFFRACTION8( CHAIN A AND RESID 70:163 )A70 - 163
9X-RAY DIFFRACTION9( CHAIN A AND RESID 164:230 )A164 - 230
10X-RAY DIFFRACTION10( CHAIN A AND RESID 231:302 )A231 - 302
11X-RAY DIFFRACTION11( CHAIN A AND RESID 303:344 )A303 - 344
12X-RAY DIFFRACTION12( CHAIN A AND RESID 345:367 )A345 - 367
13X-RAY DIFFRACTION13( CHAIN A AND RESID 403:403 )A403
14X-RAY DIFFRACTION14( CHAIN B AND RESID 2:22 )B2 - 22
15X-RAY DIFFRACTION15( CHAIN B AND RESID 23:69 )B23 - 69
16X-RAY DIFFRACTION16( CHAIN B AND RESID 70:120 )B70 - 120
17X-RAY DIFFRACTION17( CHAIN B AND RESID 121:163 )B121 - 163
18X-RAY DIFFRACTION18( CHAIN B AND RESID 164:230 )B164 - 230
19X-RAY DIFFRACTION19( CHAIN B AND RESID 231:248 )B231 - 248

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