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

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Basic information

Entry
Database: PDB / ID: 6dxb
TitleCrystal structure of chalcone synthase from Arabidopsis thaliana
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: 1.549 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 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Chalcone synthase
D: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)172,8114
Polymers172,8114
Non-polymers00
Water30,2651680
1
A: Chalcone synthase
C: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)86,4052
Polymers86,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-15 kcal/mol
Surface area26940 Å2
MethodPISA
2
B: Chalcone synthase
D: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)86,4052
Polymers86,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-14 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.640, 137.560, 108.560
Angle α, β, γ (deg.)90.000, 95.590, 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: 43202.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CHS, TT4, At5g13930, MAC12.11, MAC12.14 / Plasmid: pHis8-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13114, chalcone synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1680 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES (pH 7.5), 0.3 M ammonium acetate, 14% (v/v) PEG 8000, and 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2010
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.549→38.681 Å / Num. obs: 227280 / % possible obs: 98.48 % / Redundancy: 1.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.04372 / Rpim(I) all: 0.04372 / Rrim(I) all: 0.06182 / Net I/σ(I): 10.17
Reflection shellResolution: 1.549→1.604 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.2437 / Mean I/σ(I) obs: 2.78 / Num. unique obs: 21992 / CC1/2: 0.837 / Rpim(I) all: 0.2437 / Rrim(I) all: 0.3447 / % possible all: 95.43

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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: 1.549→38.681 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.18
RfactorNum. reflection% reflection
Rfree0.1633 1963 8.6 %
Rwork0.1407 --
obs0.1409 227260 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.48 Å2 / Biso mean: 17.52 Å2 / Biso min: 5.25 Å2
Refinement stepCycle: final / Resolution: 1.549→38.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11944 0 0 1680 13624
Biso mean---28.32 -
Num. residues----1554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912306
X-RAY DIFFRACTIONf_angle_d1.26416676
X-RAY DIFFRACTIONf_chiral_restr0.051892
X-RAY DIFFRACTIONf_plane_restr0.0072160
X-RAY DIFFRACTIONf_dihedral_angle_d12.9164576
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.549-1.58770.19971330.1993153311546494
1.5877-1.63070.19821370.1799160141615198
1.6307-1.67860.19771370.1672160921622999
1.6786-1.73280.20111420.1563160981624099
1.7328-1.79480.17451410.149161281626999
1.7948-1.86660.16911390.1475160601619998
1.8666-1.95160.17111430.1418161101625398
1.9516-2.05450.16121360.1361160071614398
2.0545-2.18320.16251390.1316160711621098
2.1832-2.35170.14661420.1274160851622799
2.3517-2.58830.16261430.1324162201636399
2.5883-2.96270.14671430.13851627116414100
2.9627-3.73230.15261430.13841634916492100
3.7323-38.69260.15941450.13231646116606100
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)
10.8940.65630.79861.33770.88821.50720.0045-0.0804-0.00330.0463-0.05310.01490.1049-0.10450.0590.05430.00810.01620.06860.00450.059313.5837-20.757716.3422
27.74370.44775.3071.8136-0.02073.7810.10810.0365-0.2478-0.320.02280.04370.386-0.0657-0.32850.2387-0.04160.00070.1101-0.02210.10813.5151-40.0806-6.0147
30.5867-0.92241.14722.222-1.50582.62760.0286-0.0518-0.0588-0.15610.01040.2020.1981-0.2631-0.03450.1245-0.0639-0.01280.1429-0.02380.1386-1.0732-27.75991.4857
41.3247-0.02853.09330.3263-0.22618.82980.0015-0.1065-0.00110.00710.030.10150.1085-0.4037-0.07730.0631-0.01440.00990.0992-0.0060.08813.8056-16.778614.6119
50.22250.04020.11350.51390.08790.63280.00020.0347-0.027-0.03580.0083-0.00670.0406-0.0253-0.00750.0577-0.01380.00120.075-0.00010.062212.9101-15.417213.0966
60.8211-0.182-0.71210.9950.84781.76960.0048-0.1074-0.05150.1540.0148-0.07030.12820.1184-0.00440.09990.0024-0.02530.10780.01490.104924.5539-18.479726.7171
75.1447-3.11791.44191.899-0.91440.44510.20840.3963-0.3619-0.2584-0.11330.12420.24110.1091-0.1090.15830.0129-0.02120.1357-0.05440.154418.125-23.253-5.2665
82.1138-0.04361.19431.46990.02433.60820.00910.0833-0.1043-0.01750.0296-0.25630.26240.3668-0.00610.10770.0359-0.0040.0676-0.01110.147732.2309-30.971712.6427
94.6805-0.4017-0.55210.8380.54091.8416-0.015-0.0977-0.35110.0260.0654-0.16510.30810.0783-0.04470.1683-0.0029-0.00220.0511-0.00430.133820.6933-37.715612.6342
100.92050.05430.0051.0551-0.59592.6916-0.0242-0.0856-0.0870.14740.0013-0.07830.19950.02880.01950.12070.0124-0.0120.0505-0.00540.098422.5418-29.040721.1537
111.3264-0.25680.88581.1723-0.32821.3029-0.01640.0670.0411-0.0392-0.0363-0.0799-0.120.09680.1140.03940.00340.02760.0632-0.02070.061724.162.24282.2261
123.66230.65453.60780.92811.08014.1793-0.2112-0.22860.2994-0.5443-0.19250.5791-0.5062-0.45590.33880.27160.1037-0.13110.2068-0.03490.24110.396115.1178-12.1666
131.05890.40940.74130.84260.36231.09360.00170.0824-0.0024-0.1475-0.01310.0197-0.06420.02460.0080.0909-0.00170.00960.09410.00660.061717.2968-0.1124-10.5329
140.26720.02760.23390.45280.00020.8681-0.01840.0237-0.0152-0.0411-0.0024-0.0169-0.03590.002-0.00680.0494-0.00570.00070.08330.0030.085522.3983-4.15042.693
150.1034-0.076-0.17960.4250.04380.64210.0194-0.03520.0332-0.0315-0.0255-0.0219-0.0705-0.06620.05490.07310.005-0.00660.07050.00660.078416.31291.96619.4503
163.63250.70161.41721.6580.57682.5676-0.0137-0.30340.21780.071-0.01020.0464-0.1241-0.0701-0.00540.09470.0118-0.0120.0476-0.00780.105316.885114.035118.6336
172.3906-0.2876-0.66021.17111.19553.41960.0078-0.05260.2588-0.07690.0104-0.0077-0.39890.0049-0.00350.15640.0023-0.02450.06320.02090.140317.10318.62076.1315
185.40851.92361.92822.79462.08752.6019-0.10030.08260.1326-0.22340.0663-0.0957-0.28370.1581-0.05220.1066-0.02450.00040.08830.01690.091628.547412.81013.7727
192.50061.145-0.1611.8451-0.03851.1516-0.0506-0.01080.12660.00840.0349-0.1027-0.19940.10180.00060.0862-0.0173-0.01650.0668-0.00060.084925.645511.765814.4394
200.6622-0.2592-0.19070.59380.02020.4323-0.01960.0009-0.0295-0.0307-0.010.01190.0477-0.01240.02880.0719-0.01710.00160.058-0.0020.076-8.198-30.824453.7727
211.5099-0.7899-1.19930.74940.54671.5086-0.0432-0.0961-0.00540.03240.0289-0.0120.0920.0127-0.01890.0775-0.00880.00690.0580.0020.0926-9.5993-31.2259.2226
220.521-0.0226-0.19740.8202-0.15850.7672-0.0508-0.1132-0.07510.11770.0042-0.00090.08910.01820.04980.10320.02310.01150.09220.01160.0817-3.7153-34.388471.1157
230.55810.2748-0.69431.1026-0.84732.00450.0535-0.05240.06970.0837-0.01220.043-0.12880.0205-0.05780.03730.0282-0.0180.0559-0.02340.061-9.6658-3.084960.1893
244.5436-0.7132-3.9321.72740.81163.43740.19490.36140.1523-0.2261-0.1686-0.027-0.0372-0.1981-0.06060.15580.07490.00480.17180.01980.0928-5.42135.609431.6556
250.2894-0.0769-0.20810.3446-0.10910.8272-0.0091-0.06140.04480.0506-0.0031-0.0588-0.04880.04890.0050.0786-0.0013-0.01690.0768-0.02350.0750.4598-5.887458.0758
260.44670.0319-0.32570.4026-0.2080.43840.01210.02420.0139-0.00810.00390.0336-0.0292-0.0777-0.00340.09830.0113-0.00530.0854-0.01790.0788-10.0077-8.006256.1003
270.8446-0.01720.0410.4872-0.09160.1121-0.00190.06210.05850.0108-0.02650.0424-0.0246-0.1177-0.0140.08040.0142-0.00130.06660.01190.0936-16.4893-8.804654.9837
281.9928-0.0818-1.03851.13810.33523.02110.03160.0582-0.0016-0.0894-0.06020.2206-0.0408-0.35850.02510.09010.0364-0.03050.1135-0.00410.1486-30.2872-2.537654.1345
293.23950.89840.52831.09530.29162.13040.0229-0.00490.2737-0.09580.02690.247-0.1745-0.1958-0.02130.13690.0349-0.01630.07820.00720.144-21.47946.683950.1948
303.5356-1.8966-1.76422.64542.02693.60670.0574-0.05060.1059-0.0454-0.02040.0141-0.2656-0.0007-0.05580.12130.00920.00420.0772-0.00460.0717-15.74656.675461.9753
310.8448-0.3086-0.27393.13941.59171.73220.0297-0.0420.11080.1011-0.02120.1531-0.135-0.15320.00570.09090.0370.01260.0869-0.00520.0961-24.83570.287362.0112
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 230 )A123 - 230
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 252 )A231 - 252
7X-RAY DIFFRACTION7chain 'A' and (resid 253 through 276 )A253 - 276
8X-RAY DIFFRACTION8chain 'A' and (resid 277 through 312 )A277 - 312
9X-RAY DIFFRACTION9chain 'A' and (resid 313 through 343 )A313 - 343
10X-RAY DIFFRACTION10chain 'A' and (resid 344 through 395 )A344 - 395
11X-RAY DIFFRACTION11chain 'C' and (resid 8 through 48 )C8 - 48
12X-RAY DIFFRACTION12chain 'C' and (resid 49 through 67 )C49 - 67
13X-RAY DIFFRACTION13chain 'C' and (resid 68 through 122 )C68 - 122
14X-RAY DIFFRACTION14chain 'C' and (resid 123 through 230 )C123 - 230
15X-RAY DIFFRACTION15chain 'C' and (resid 231 through 276 )C231 - 276
16X-RAY DIFFRACTION16chain 'C' and (resid 277 through 312 )C277 - 312
17X-RAY DIFFRACTION17chain 'C' and (resid 313 through 343 )C313 - 343
18X-RAY DIFFRACTION18chain 'C' and (resid 344 through 362 )C344 - 362
19X-RAY DIFFRACTION19chain 'C' and (resid 363 through 395 )C363 - 395
20X-RAY DIFFRACTION20chain 'B' and (resid 7 through 184 )B7 - 184
21X-RAY DIFFRACTION21chain 'B' and (resid 185 through 242 )B185 - 242
22X-RAY DIFFRACTION22chain 'B' and (resid 243 through 395 )B243 - 395
23X-RAY DIFFRACTION23chain 'D' and (resid 8 through 48 )D8 - 48
24X-RAY DIFFRACTION24chain 'D' and (resid 49 through 68 )D49 - 68
25X-RAY DIFFRACTION25chain 'D' and (resid 69 through 159 )D69 - 159
26X-RAY DIFFRACTION26chain 'D' and (resid 160 through 230 )D160 - 230
27X-RAY DIFFRACTION27chain 'D' and (resid 231 through 276 )D231 - 276
28X-RAY DIFFRACTION28chain 'D' and (resid 277 through 312 )D277 - 312
29X-RAY DIFFRACTION29chain 'D' and (resid 313 through 343 )D313 - 343
30X-RAY DIFFRACTION30chain 'D' and (resid 344 through 362 )D344 - 362
31X-RAY DIFFRACTION31chain 'D' and (resid 363 through 395 )D363 - 395

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