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- PDB-7pd1: Crystal structure of the L-tyrosine-bound radical SAM tyrosine ly... -

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Basic information

Entry
Database: PDB / ID: 7pd1
TitleCrystal structure of the L-tyrosine-bound 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 / BROMIDE ION / : / METHIONINE / IRON/SULFUR CLUSTER / TYROSINE / Thiazole biosynthesis protein ThiH
Similarity search - Component
Biological speciesThermosinus carboxydivorans Nor1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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)89,42728
Polymers86,0702
Non-polymers3,35726
Water17,330962
1
A: Thiazole biosynthesis protein ThiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,77515
Polymers43,0351
Non-polymers1,74014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiazole biosynthesis protein ThiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,65213
Polymers43,0351
Non-polymers1,61712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.090, 48.850, 85.410
Angle α, β, γ (deg.)90.000, 97.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-866-

HOH

21B-963-

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 , 9 types, 988 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-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Br
#9: 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
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 962 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
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 1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.27→47.03 Å / Num. obs: 188955 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rsym value: 0.081 / Net I/σ(I): 11.56
Reflection shellResolution: 1.27→1.35 Å / Num. unique obs: 29885 / Rsym value: 0.947

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R34

4r34


Resolution: 1.27→47.03 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1698 9451 5 %
Rwork0.1499 179504 -
obs0.1509 188955 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.74 Å2 / Biso mean: 21.8651 Å2 / Biso min: 10.15 Å2
Refinement stepCycle: final / Resolution: 1.27→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5810 0 145 967 6922
Biso mean--20.86 34.33 -
Num. residues----733
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 (%)
1.27-1.280.36332840.37265391567590
1.28-1.30.32683140.322259496263100
1.3-1.310.30713130.291159656278100
1.31-1.330.28023140.270459706284100
1.33-1.350.26123140.242259436257100
1.35-1.370.24793150.229259906305100
1.37-1.390.22913120.225759226234100
1.39-1.410.24343160.223160066322100
1.41-1.430.23053150.209459716286100
1.43-1.450.21633130.195659546267100
1.45-1.480.18743170.183859996316100
1.48-1.50.21243140.176359686282100
1.5-1.530.19513170.168260276344100
1.53-1.560.18983150.162959836298100
1.56-1.60.17963140.142559576271100
1.6-1.640.1723150.146559936308100
1.64-1.680.17893160.14360096325100
1.68-1.720.16443140.139159556269100
1.72-1.770.17463160.137360076323100
1.77-1.830.16443160.136960046320100
1.83-1.890.16963180.136860346352100
1.89-1.970.17343160.135360056321100
1.97-2.060.15713160.136760056321100
2.06-2.170.1693150.129659926307100
2.17-2.30.14183180.135960406358100
2.3-2.480.16483170.139960156332100
2.48-2.730.16523190.15160686387100
2.73-3.130.16713170.147660296346100
3.13-3.940.13493220.126861176439100
3.94-47.030.1533290.138262366565100
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)
11.5169-1.36080.88773.3277-1.32761.7218-0.1443-0.39180.11860.58960.0742-0.1286-0.3474-0.06320.00480.27480.0028-0.00510.3222-0.02740.183921.8265.73153.435
20.4760.3525-0.07941.1213-0.3491.02660.0021-0.0577-0.03930.04370.0049-0.01770.1321-0.01930.00140.11530.02530.00420.1436-0.01060.122821.834-4.99837.447
31.09680.46850.58390.8241-0.15490.9954-0.14590.14140.1157-0.24920.1059-0.0503-0.24380.21910.0280.2155-0.0154-0.00560.1646-0.01050.165729.49318.3816.507
40.73270.1237-0.02121.3346-0.03821.29320.00640.01940.1984-0.06840.00470.1245-0.1175-0.07310.00410.15330.0147-0.00540.1289-0.0010.177718.92518.63721.429
51.4291-0.19840.11761.3141-0.16461.05780.1001-0.15530.11020.0656-0.04910.0594-0.0719-0.0062-0.0520.1593-0.01630.0170.15-0.03750.147520.92517.04937.459
60.9413-0.0221-0.3691.1259-0.11420.98070.022-0.1061-0.02660.0347-0.00710.0389-0.03820.0319-0.01590.1556-0.0151-0.00830.1709-0.02240.122323.9365.78837.723
70.35830.2036-0.14430.8571-0.14881.7021-0.00350.0184-0.0029-0.06680.02090.00660.06310.0289-0.00750.13090.0148-0.00630.1443-0.00950.121224.836-2.00824.662
81.2233-0.03090.31097.9672.52972.9435-0.0007-0.11150.1358-0.08080.02530.1009-0.00390.0708-0.02420.1252-0.0068-0.00060.1802-0.00060.155527.0111.59827.502
91.576-3.1454-2.15656.7324.32664.7893-0.2817-0.3567-0.05490.76240.3069-0.09820.45250.1888-0.02270.2709-0.0002-0.06720.33650.03540.177-5.306-5.34134.394
102.28570.06940.82261.7137-0.48424.6031-0.0453-0.21680.25410.17950.0424-0.1212-0.35170.103-0.01250.1535-0.0283-0.02670.1548-0.02920.163-6.53613.08524.025
110.5409-0.04930.09050.87960.11460.7083-0.0104-0.0545-0.07540.00040.009-0.00260.07190.00980.00080.1272-0.00240.00160.14140.01970.1189-15.09-10.07713.607
120.76840.25180.49943.09550.32172.6404-0.03790.0447-0.0177-0.13770.06450.30470.0641-0.2402-0.00130.09850.0134-0.00790.16250.01080.1331-25.473-3.8336.728
131.3754-0.1247-0.25361.79390.51761.4054-0.0143-0.0238-0.0393-0.17140.0556-0.1131-0.08420.2726-0.03240.2176-0.0068-0.01390.22250.01720.1391-14.6276.212-0.236
141.929-1.20030.79576.1972-7.33369.2383-0.1747-0.2081-0.0411-0.10950.1519-0.2177-0.071-0.21410.00920.1506-0.00470.00260.1674-0.00360.1363-19.501-10.80612.149
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:22 )A2 - 22
2X-RAY DIFFRACTION2( CHAIN A AND RESID 23:92 )A23 - 92
3X-RAY DIFFRACTION3( CHAIN A AND RESID 93:120 )A93 - 120
4X-RAY DIFFRACTION4( CHAIN A AND RESID 121:163 )A121 - 163
5X-RAY DIFFRACTION5( CHAIN A AND RESID 164:214 )A164 - 214
6X-RAY DIFFRACTION6( CHAIN A AND RESID 215:275 )A215 - 275
7X-RAY DIFFRACTION7( CHAIN A AND RESID 276:367 )A276 - 367
8X-RAY DIFFRACTION8( CHAIN A AND RESID 403:404 )A403 - 404
9X-RAY DIFFRACTION9( CHAIN B AND RESID 1:22 )B1 - 22
10X-RAY DIFFRACTION10( CHAIN B AND RESID 23:69 )B23 - 69
11X-RAY DIFFRACTION11( CHAIN B AND RESID 70:309 )B70 - 309
12X-RAY DIFFRACTION12( CHAIN B AND RESID 310:344 )B310 - 344
13X-RAY DIFFRACTION13( CHAIN B AND RESID 345:367 )B345 - 367
14X-RAY DIFFRACTION14( CHAIN B AND RESID 403:404 )B403 - 404

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