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

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Basic information

Entry
Database: PDB / ID: 6dxd
TitleCrystal structure of chalcone synthase from Arabidopsis thaliana - C347S mutant
ComponentsChalcone synthase
KeywordsTRANSFERASE / Thiolase / Flavonoid / Polyketide synthase
Function / homology
Function and homology information


regulation of anthocyanin biosynthetic process / plant-type vacuole membrane / : / chalcone synthase / auxin polar transport / naringenin-chalcone synthase activity / response to jasmonic acid / response to auxin / flavonoid biosynthetic process / response to gravity ...regulation of anthocyanin biosynthetic process / plant-type vacuole membrane / : / chalcone synthase / auxin polar transport / naringenin-chalcone synthase activity / response to jasmonic acid / response to auxin / flavonoid biosynthetic process / response to gravity / response to UV-B / response to wounding / response to oxidative stress / endoplasmic reticulum / nucleus
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-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 / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-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: 1.59 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
B: Chalcone synthase
C: Chalcone synthase
D: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)172,7464
Polymers172,7464
Non-polymers00
Water32,8771825
1
A: Chalcone synthase
C: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)86,3732
Polymers86,3732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-15 kcal/mol
Surface area27140 Å2
MethodPISA
2
B: Chalcone synthase
D: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)86,3732
Polymers86,3732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-13 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.860, 138.220, 108.900
Angle α, β, γ (deg.)90.000, 95.730, 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: 43186.598 Da / Num. of mol.: 4 / Mutation: 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: pHis8-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13114, chalcone synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1825 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
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: Apr 27, 2011
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: 1.59→32.92 Å / Num. obs: 201521 / % possible obs: 93.32 % / Redundancy: 1.8 % / Biso Wilson estimate: 14.09 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.05533 / Rpim(I) all: 0.05533 / Rrim(I) all: 0.07824 / Net I/σ(I): 8.04
Reflection shellResolution: 1.59→1.647 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.3447 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 17370 / CC1/2: 0.699 / Rpim(I) all: 0.3447 / Rrim(I) all: 0.4874 / % possible all: 65.39

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.68 Å34.14 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASER2.8.1phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→32.92 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.69
RfactorNum. reflection% reflection
Rfree0.1685 1855 9.2 %
Rwork0.1451 --
obs0.1453 201487 93.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.1 Å2 / Biso mean: 22.5236 Å2 / Biso min: 6.19 Å2
Refinement stepCycle: final / Resolution: 1.59→32.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11956 0 0 1825 13781
Biso mean---30.64 -
Num. residues----1556
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.59-1.6330.2882900.2512106951078565
1.633-1.6810.2451040.2309110651116968
1.681-1.73530.23821400.2055151391527992
1.7353-1.79730.22721520.1945160481620098
1.7973-1.86930.1971510.1739160921624398
1.8693-1.95430.1981480.1577162241637298
1.9543-2.05740.2011520.1461161061625899
2.0574-2.18620.1741500.1371162661641699
2.1862-2.3550.15621540.1277162261638099
2.355-2.59190.17071510.1304163521650399
2.5919-2.96680.15791540.1338163501650499
2.9668-3.73710.14631530.13351646416617100
3.7371-34.14510.12911560.12921660516761100
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)
10.58410.3412-0.71581.026-0.76261.84660.0834-0.06330.03560.0978-0.04880.0267-0.15060.0318-0.04750.04040.0214-0.01490.0701-0.01940.082822.91591.91836.629
23.1108-1.2285-4.57812.57151.67758.05810.25470.41640.176-0.2895-0.2429-0.0242-0.1377-0.334-0.03960.15340.06930.0160.16380.01260.105327.513811.1027-22.6224
31.3916-1.3295-0.83761.96210.84131.46590.04520.00480.1146-0.0641-0.0152-0.107-0.07440.1065-0.05120.1012-0.01080.0020.0819-0.00250.104636.23785.2331-10.8196
41.2796-0.6618-2.0730.85081.39524.61120.0622-0.15580.10850.02150.068-0.104-0.08090.2435-0.12840.0898-0.0046-0.01070.1045-0.01890.089133.55670.91426.338
50.30160.0168-0.38530.3994-0.08690.70390.0226-0.01420.01150.0053-0.00590.0072-0.0304-0.0181-0.00960.09980.0041-0.00440.0964-0.01420.086625.4355-3.816.2324
61.30410.32081.19790.1642-0.05843.03440.0152-0.23280.11830.1311-0.00960.0169-0.1012-0.2024-0.02810.12840.01950.01590.1256-0.03230.111312.39511.471917.7456
78.8186-1.960.33760.51970.00230.06710.10540.46440.1125-0.216-0.1315-0.01820.0179-0.10450.01110.11830.02010.00270.16120.01840.107319.3918-7.6147-13.4296
85.0066-0.7131-4.64451.02680.74954.3218-0.06150.1127-0.2203-0.0807-0.14190.26750.0291-0.21340.25740.10650.0015-0.0350.1551-0.01710.17161.1577-0.7275-2.0881
91.6359-0.0548-0.96530.6003-0.14312.2776-0.00480.18750.08-0.03890.00540.2247-0.1835-0.2602-0.02270.11170.0357-0.01690.1265-0.0130.1674.6238.7591-2.1494
101.445-0.0007-0.88461.33740.57372.24360.0369-0.08370.17960.08480.0140.1165-0.1995-0.0363-0.03180.1120.01990.00230.0646-0.02350.1116.459113.02863.2477
111.0764-0.4948-0.33932.97351.48512.4853-0.0082-0.02210.11390.09330.020.1856-0.1075-0.0846-0.01570.08350.02610.00730.0994-0.00980.1197.96545.85227.8643
120.46610.35560.33731.04480.5731.1342-0.0098-0.0944-0.03870.0289-0.05090.00570.1394-0.1050.03130.0873-0.00750.01070.06970.00240.0896-8.4213-15.371-37.8527
134.68260.80064.50032.74970.74098.12280.15660.1417-0.2541-0.21630.01030.13590.62940.1324-0.27280.2672-0.06870.00970.1191-0.0160.1388-17.8644-35.173-60.0986
140.5211-0.55490.57821.6141-0.76831.8036-0.00380.0494-0.0827-0.2406-0.00130.17770.2163-0.26690.00210.1727-0.0659-0.01880.1628-0.02050.1594-23.0292-22.427-52.7554
150.93160.13071.79250.37060.06295.4747-0.0165-0.05560.004-0.03990.03150.10180.1267-0.3588-0.02170.0876-0.02050.00330.1045-0.00630.1069-18.2107-11.3896-39.5909
160.5856-0.10570.2040.7406-0.06771.44830.01010.0512-0.039-0.02830.03170.06170.0031-0.14170.02120.0865-0.01080.00260.095-0.00140.1-12.5954-2.8112-35.5792
170.30690.12520.08110.44680.17660.6319-0.03590.0924-0.0371-0.07580.0422-0.00940.09290.0396-0.0170.1057-0.0207-0.00210.0802-0.00520.0784-7.2034-13.8709-44.0393
181.1281-0.2542-0.81340.71450.73581.0862-0.0186-0.1931-0.03870.12850.0572-0.02170.12290.1840.0140.13160.0066-0.02420.12350.01560.1062.5244-13.0642-27.3784
194.1106-2.34721.18291.3491-0.69550.35750.1420.419-0.296-0.2398-0.08770.14830.18960.1385-0.00070.17250.0042-0.02190.1661-0.05690.167-3.4952-17.6701-59.6687
201.27880.11280.54981.12170.02432.3568-0.04010.051-0.1237-0.00790.0505-0.1990.26770.2838-0.00580.14470.0459-0.00450.1014-0.01780.161810.2196-25.6001-41.5131
213.2509-0.4206-0.28271.00280.38971.4737-0.0155-0.0433-0.33060.04640.0464-0.12880.33440.08970.00610.20310.00750.00110.0789-0.00620.1624-1.2813-32.3792-41.5246
222.2183-0.81311.42631.3984-1.01845.0571-0.0187-0.0805-0.08610.16240.02880.0390.2072-0.0005-0.02350.1726-0.01210.00490.0691-0.00730.1137-5.9557-25.2549-31.6216
230.94180.211-0.16581.4755-1.12633.668-0.0392-0.0403-0.09650.14240.0243-0.0860.17320.11670.0130.12350.0276-0.01010.0634-0.00420.11744.6884-22.6918-33.7849
241.6873-0.4952-0.55880.8440.22740.6108-0.06340.0141-0.09820.0346-0.02940.0730.0905-0.06190.07040.0855-0.0101-0.00160.06360.02570.072720.6561-26.39215.7462
256.680.4964-4.27642.5094-1.17184.9873-0.0092-0.3048-0.1976-0.0788-0.1576-0.24310.30920.79020.06590.13380.05230.03110.19460.02990.188148.4114-36.76-2.838
261.34510.829-1.38773.1878-2.74862.8159-0.05210.1008-0.0877-0.2661-0.1158-0.23210.18680.05170.11390.16290.0090.0380.0941-0.00380.141635.519-31.0515-10.1977
276.47162.4632-4.35831.4965-1.68233.4508-0.14730.2163-0.174-0.15560.04810.0180.1605-0.20360.12120.0966-0.0034-0.00530.0858-0.01450.104719.1996-25.8396-4.9969
280.79920.0128-0.43040.7715-0.1441.1562-0.0124-0.0087-0.0014-0.0378-0.01740.060.03360.02240.02460.07690.0004-0.00180.0908-0.01110.114115.6642-18.50213.7155
291.5757-1.012-1.86011.17470.61992.76490.0129-0.12710.1155-0.02380.0103-0.21970.06860.3599-0.0480.09420.0130.00910.08420.00890.153836.0223-27.48470.0215
301.5938-0.25870.81160.38570.28270.9113-0.001-0.2398-0.09720.1037-0.02470.18570.1111-0.17360.02660.1311-0.01390.04630.13760.00880.161911.2915-25.038917.9411
310.1931-0.15371.00380.5844-1.96717.9637-0.0087-0.00730.0426-0.0601-0.1646-0.17030.10660.55120.11170.10270.03930.00860.17230.01420.122441.1395-17.64155.5845
324.8685-0.2224-6.23351.43640.20397.99020.0748-0.2129-0.05530.2018-0.1005-0.1407-0.16880.1402-0.03330.14490.0084-0.02440.17320.0160.136132.6259-23.330625.7871
333.0447-0.3478-1.74210.5909-0.17982.599-0.0621-0.2184-0.15750.1527-0.0101-0.11950.04260.17940.08390.14160.00980.01470.12210.03830.133331.8444-32.875622.7423
342.73660.7422-0.83141.54770.18381.7942-0.0771-0.086-0.19480.0998-0.0128-0.00530.2142-0.05450.0620.1256-0.00070.02580.06470.01370.122124.579-37.398412.0102
351.69771.5358-0.3842.9546-0.65410.9406-0.0919-0.1102-0.15280.12510.02120.03380.1183-0.03570.07660.10950.01480.03690.09490.01870.104521.5679-29.764320.781
361.3415-0.44071.05461.1355-0.43821.8161-0.05810.00670.0472-0.11120.01120.0851-0.2228-0.09350.04240.09290.01110.00530.0816-0.01460.0945-5.556311.8156-56.4664
370.4044-0.01730.32410.3781-0.06050.9267-0.01580.0194-0.0009-0.07680.00940.0002-0.0196-0.04020.00160.0871-0.00930.00040.105500.1007-1.2562.5826-56.1615
380.1363-0.1318-0.27990.37290.05520.81130.0393-0.0310.0312-0.0303-0.0308-0.0309-0.0508-0.07730.01920.09310.0004-0.00450.07620.01230.0917-4.90097.3393-44.6488
391.1036-0.00340.18890.54150.15031.1748-0.0263-0.03570.1125-0.03810.0275-0.0303-0.2060.0249-0.00660.1139-0.0194-0.01470.0660.00240.1182-0.836420.0076-42.6071
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 68 )A49 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 95 )A69 - 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 296 )A277 - 296
9X-RAY DIFFRACTION9chain 'A' and (resid 297 through 326 )A297 - 326
10X-RAY DIFFRACTION10chain 'A' and (resid 327 through 362 )A327 - 362
11X-RAY DIFFRACTION11chain 'A' and (resid 363 through 395 )A363 - 395
12X-RAY DIFFRACTION12chain 'B' and (resid 7 through 48 )B7 - 48
13X-RAY DIFFRACTION13chain 'B' and (resid 49 through 67 )B49 - 67
14X-RAY DIFFRACTION14chain 'B' and (resid 68 through 95 )B68 - 95
15X-RAY DIFFRACTION15chain 'B' and (resid 96 through 122 )B96 - 122
16X-RAY DIFFRACTION16chain 'B' and (resid 123 through 159 )B123 - 159
17X-RAY DIFFRACTION17chain 'B' and (resid 160 through 230 )B160 - 230
18X-RAY DIFFRACTION18chain 'B' and (resid 231 through 252 )B231 - 252
19X-RAY DIFFRACTION19chain 'B' and (resid 253 through 276 )B253 - 276
20X-RAY DIFFRACTION20chain 'B' and (resid 277 through 312 )B277 - 312
21X-RAY DIFFRACTION21chain 'B' and (resid 313 through 343 )B313 - 343
22X-RAY DIFFRACTION22chain 'B' and (resid 344 through 362 )B344 - 362
23X-RAY DIFFRACTION23chain 'B' and (resid 363 through 395 )B363 - 395
24X-RAY DIFFRACTION24chain 'C' and (resid 7 through 48 )C7 - 48
25X-RAY DIFFRACTION25chain 'C' and (resid 49 through 68 )C49 - 68
26X-RAY DIFFRACTION26chain 'C' and (resid 69 through 95 )C69 - 95
27X-RAY DIFFRACTION27chain 'C' and (resid 96 through 122 )C96 - 122
28X-RAY DIFFRACTION28chain 'C' and (resid 123 through 201 )C123 - 201
29X-RAY DIFFRACTION29chain 'C' and (resid 202 through 230 )C202 - 230
30X-RAY DIFFRACTION30chain 'C' and (resid 231 through 252 )C231 - 252
31X-RAY DIFFRACTION31chain 'C' and (resid 253 through 276 )C253 - 276
32X-RAY DIFFRACTION32chain 'C' and (resid 277 through 296 )C277 - 296
33X-RAY DIFFRACTION33chain 'C' and (resid 297 through 326 )C297 - 326
34X-RAY DIFFRACTION34chain 'C' and (resid 327 through 362 )C327 - 362
35X-RAY DIFFRACTION35chain 'C' and (resid 363 through 395 )C363 - 395
36X-RAY DIFFRACTION36chain 'D' and (resid 7 through 68 )D7 - 68
37X-RAY DIFFRACTION37chain 'D' and (resid 69 through 230 )D69 - 230
38X-RAY DIFFRACTION38chain 'D' and (resid 231 through 276 )D231 - 276
39X-RAY DIFFRACTION39chain 'D' and (resid 277 through 395 )D277 - 395

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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