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- PDB-6dxe: Crystal structure of chalcone synthase from Arabidopsis thaliana ... -

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Basic information

Entry
Database: PDB / ID: 6dxe
TitleCrystal structure of chalcone synthase from Arabidopsis thaliana - M64I F170S G173A S213G Q217A T270V C347S mutant
ComponentsChalcone synthase
KeywordsTRANSFERASE / Thiolase / Flavonoid / Polyketide synthase
Function / homology
Function and homology information


regulation of anthocyanin biosynthetic process / chalcone biosynthetic process / chalcone synthase / naringenin-chalcone synthase activity / plant-type vacuole membrane / flavonoid biosynthetic process / auxin polar transport / polyketide biosynthetic process / response to auxin / response to jasmonic acid ...regulation of anthocyanin biosynthetic process / chalcone biosynthetic process / chalcone synthase / naringenin-chalcone synthase activity / plant-type vacuole membrane / flavonoid biosynthetic process / auxin polar transport / polyketide biosynthetic process / response to auxin / response to jasmonic acid / response to UV-B / acyltransferase activity, transferring groups other than amino-acyl groups / response to gravity / response to wounding / response to oxidative stress / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like ...Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.608 Å
AuthorsLiou, G. / Chiang, Y.C. / Wang, Y. / Weng, J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1709616 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants.
Authors: Liou, G. / Chiang, Y.C. / Wang, Y. / Weng, J.K.
History
DepositionJun 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chalcone synthase
C: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)86,0352
Polymers86,0352
Non-polymers00
Water15,475859
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-17 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.800, 55.900, 100.210
Angle α, β, γ (deg.)90.000, 92.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chalcone synthase / Naringenin-chalcone synthase / Protein TRANSPARENT TESTA 4


Mass: 43017.441 Da / Num. of mol.: 2 / Mutation: M64I, F170S, G173A, S213G, Q217A, T270V, C347S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CHS, TT4, At5g13930, MAC12.11, MAC12.14 / Plasmid: pHis8-4B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13114, chalcone synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.125 NaSCN, 20% (v/v) PEG 3350, and 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2018
RadiationMonochromator: single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.608→60.11 Å / Num. obs: 175827 / % possible obs: 91.6 % / Redundancy: 2.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04526 / Rpim(I) all: 0.03089 / Rrim(I) all: 0.05506 / Net I/σ(I): 11.1
Reflection shellResolution: 1.608→1.665 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.5779 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 7995 / CC1/2: 0.778 / Rpim(I) all: 0.392 / Rrim(I) all: 0.7013 / % possible all: 76.72

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.608→60.107 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.2015 3515 2 %
Rwork0.1698 --
obs0.1704 175827 85.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.54 Å2 / Biso mean: 21.36 Å2 / Biso min: 7.13 Å2
Refinement stepCycle: final / Resolution: 1.608→60.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5956 0 0 859 6815
Biso mean---31.6 -
Num. residues----778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016188
X-RAY DIFFRACTIONf_angle_d1.2588395
X-RAY DIFFRACTIONf_chiral_restr0.051959
X-RAY DIFFRACTIONf_plane_restr0.0061088
X-RAY DIFFRACTIONf_dihedral_angle_d13.892313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.608-1.630.24531100.2645728583872
1.63-1.65330.28711250.26095894601973
1.6533-1.6780.31511150.25355932604774
1.678-1.70420.25081570.24796110626776
1.7042-1.73220.26671160.24016297641377
1.7322-1.7620.25011450.23556153629878
1.762-1.79410.24721150.2326476659180
1.7941-1.82860.25691550.2346681683683
1.8286-1.86590.29641340.22876770690484
1.8659-1.90650.2361430.22576876701986
1.9065-1.95090.25231180.216603672182
1.9509-1.99960.21071580.19777308746691
1.9996-2.05370.22841540.1917408756292
2.0537-2.11410.2381400.17747390753092
2.1141-2.18240.22381410.16967344748591
2.1824-2.26040.19791350.15957368750391
2.2604-2.35090.18811460.15417292743891
2.3509-2.45790.21441360.1517279741591
2.4579-2.58750.15551560.14857295745190
2.5875-2.74960.17361560.15966785694185
2.7496-2.96190.20191450.15867455760092
2.9619-3.25990.17171680.15677546771494
3.2599-3.73160.15381510.14357518766994
3.7316-4.70110.19781540.13077407756192
4.7011-60.14890.1661420.14147397753992
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)
10.59360.3158-0.09420.79520.03031.24450.0091-0.25070.10420.1323-0.10120.1259-0.16190.01420.06220.0990.00940.03020.1324-0.06010.1391-9.71395.891130.5391
24.7072-0.4858-0.7754.8173-3.64026.00680.02830.25250.2527-0.3138-0.08020.4234-0.0114-0.2557-0.0270.21760.0733-0.08070.1387-0.03380.2385-25.378812.1274.2055
31.37250.5141-1.00740.6629-0.68871.5922-0.05570.05630.4594-0.0130.08440.2229-0.2711-0.1578-0.0390.21660.0632-0.04580.1361-0.03760.2852-16.870919.403214.8642
40.66440.5612-0.95941.8967-2.85766.17910.0935-0.1410.35460.18510.01020.2112-0.465-0.2119-0.03950.1780.0260.00420.1378-0.08120.1847-8.300816.42830.0724
50.48690.1629-0.72640.7954-0.39381.33370.0522-0.30740.19170.0864-0.1380.0312-0.22940.14030.01290.1458-0.00650.00440.1967-0.07090.1240.101212.965635.6572
60.85640.04580.00030.5646-0.09450.5210.0377-0.0770.0786-0.0447-0.09210.0668-0.02380.00290.0520.11470.02990.00880.0988-0.02870.1041-6.47035.804125.0471
70.76110.30370.8971.68931.37925.16450.091-0.407-0.01730.2634-0.18180.10230.2699-0.0740.11460.1436-0.01990.02160.21040.00680.1147-7.0445-5.084740.9113
81.67772.6682-0.18964.3994-0.22360.0343-0.20130.230.0642-0.65440.15090.14050.15960.00430.01440.24610.0295-0.01650.1384-0.0010.1093-5.38682.38668.6518
91.55840.1804-0.03052.5925-1.21253.71730.0089-0.0069-0.2642-0.1472-0.0529-0.0020.5375-0.02830.02680.1794-0.0043-0.00690.0867-0.01270.1338-13.2938-14.484923.8254
101.9874-0.8206-0.40297.63241.57983.5897-0.0111-0.0695-0.1973-0.0532-0.01380.51740.2326-0.28430.020.09360.0222-0.01580.1253-0.01790.1665-22.7319-5.422122.44
112.12770.4956-0.97532.3238-0.92813.28290.0477-0.20460.00120.1025-0.09010.20690.0981-0.21130.03980.0856-0.0195-0.010.1271-0.03790.095-15.8841-5.232932.4006
120.6524-0.06380.33520.668-0.1570.7806-0.001-0.1541-0.1449-0.0353-0.2618-0.2760.04380.42470.2260.11620.05780.00460.21080.03940.099417.11891.8823.2665
131.17810.3392-0.25422.5776-1.68121.1051-0.36710.07770.39490.4249-0.3036-0.3457-0.68850.72110.51210.3023-0.1339-0.11450.34570.09540.249526.410730.480211.0331
141.00850.10440.19411.4836-0.77731.0893-0.10910.04370.006-0.1671-0.0231-0.071-0.02080.28160.10920.14530.03340.02870.21660.03740.096717.213310.12719.6422
151.7701-0.14770.32141.05170.32070.75360.01130.0475-0.2055-0.1547-0.107-0.09120.18380.15510.05380.14690.06840.040.1340.02430.11217.7913-5.228417.9111
161.01790.3753-0.13670.6318-0.3581.24960.0249-0.19840.03420.0578-0.1472-0.0887-0.08440.26920.09520.09330.01890.00310.19770.02330.090713.61617.94825.529
173.2854-2.98932.91748.4948-7.51319.3328-0.1381-0.75030.3410.41720.1265-0.0337-0.41470.0222-0.00680.1732-0.0588-0.01210.4266-0.09050.206319.834914.315443.2422
181.1856-0.36081.38990.2125-0.16862.4892-0.0301-0.31220.20170.1883-0.0871-0.1331-0.34550.57790.16390.1631-0.0682-0.03090.44980.03220.191128.369913.258137.8438
192.4427-2.1304-0.46893.8701-0.67041.15590.0206-0.12440.09130.0817-0.0781-0.3067-0.05110.45020.02210.0854-0.0010.00220.36490.06470.146829.67536.262626.3413
201.5065-0.19620.63410.4166-0.25820.77430.067-0.4534-0.0660.1188-0.1051-0.0676-0.15240.49780.06240.02550.0524-0.02260.4820.11330.157324.38843.207236.6216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 48 )A7 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 67 )A49 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 95 )A68 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 122 )A96 - 122
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 159 )A123 - 159
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 230 )A160 - 230
7X-RAY DIFFRACTION7chain 'A' and (resid 231 through 252 )A231 - 252
8X-RAY DIFFRACTION8chain 'A' and (resid 253 through 276 )A253 - 276
9X-RAY DIFFRACTION9chain 'A' and (resid 277 through 312 )A277 - 312
10X-RAY DIFFRACTION10chain 'A' and (resid 313 through 343 )A313 - 343
11X-RAY DIFFRACTION11chain 'A' and (resid 344 through 395 )A344 - 395
12X-RAY DIFFRACTION12chain 'C' and (resid 7 through 48 )C7 - 48
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 66 )C49 - 66
14X-RAY DIFFRACTION14chain 'C' and (resid 67 through 122 )C67 - 122
15X-RAY DIFFRACTION15chain 'C' and (resid 123 through 159 )C123 - 159
16X-RAY DIFFRACTION16chain 'C' and (resid 160 through 276 )C160 - 276
17X-RAY DIFFRACTION17chain 'C' and (resid 277 through 296 )C277 - 296
18X-RAY DIFFRACTION18chain 'C' and (resid 297 through 326 )C297 - 326
19X-RAY DIFFRACTION19chain 'C' and (resid 327 through 362 )C327 - 362
20X-RAY DIFFRACTION20chain 'C' and (resid 363 through 395 )C363 - 395

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