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- PDB-6dx7: Crystal structure of chalcone synthase from Physcomitrella patens -

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Basic information

Entry
Database: PDB / ID: 6dx7
TitleCrystal structure of chalcone synthase from Physcomitrella patens
ComponentsChalcone synthase
KeywordsTRANSFERASE / Thiolase / Flavonoid / Polyketide synthase
Function / homology
Function and homology information


: / chalcone synthase / naringenin-chalcone synthase activity / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
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 speciesPhyscomitrella patens subsp. patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.61 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 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
E: Chalcone synthase
F: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)255,7746
Polymers255,7746
Non-polymers00
Water1,06359
1
A: Chalcone synthase
B: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)85,2582
Polymers85,2582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-12 kcal/mol
Surface area26440 Å2
MethodPISA
2
C: Chalcone synthase

D: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)85,2582
Polymers85,2582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6000 Å2
ΔGint-9 kcal/mol
Surface area26560 Å2
MethodPISA
3
E: Chalcone synthase
F: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)85,2582
Polymers85,2582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-8 kcal/mol
Surface area26560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.600, 192.830, 195.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Chalcone synthase


Mass: 42629.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrella patens subsp. patens (plant)
Gene: PHYPA_029015 / Plasmid: pHis8-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2VAZ3, chalcone synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.1 M MES (pH 6.9), 18% (v/v) PEG 20000, and 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 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: 2.61→37.011 Å / Num. obs: 82406 / % possible obs: 98.95 % / Redundancy: 2 % / Biso Wilson estimate: 47.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.03961 / Rpim(I) all: 0.03961 / Rrim(I) all: 0.05602 / Net I/σ(I): 14.31
Reflection shellResolution: 2.61→2.703 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.4442 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 7763 / CC1/2: 0.747 / Rpim(I) all: 0.4442 / Rrim(I) all: 0.6282 / % possible all: 94.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→37.011 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2626 1967 2.39 %
Rwork0.181 80409 -
obs0.183 82376 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 358.19 Å2 / Biso mean: 70.8323 Å2 / Biso min: 24.96 Å2
Refinement stepCycle: final / Resolution: 2.61→37.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17592 0 0 59 17651
Biso mean---58.93 -
Num. residues----2322
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 (%)
2.61-2.67530.3961210.32745403552494
2.6753-2.74760.37291330.29225405553894
2.7476-2.82840.37651410.26395575571698
2.8284-2.91970.37151420.249457275869100
2.9197-3.0240.30981460.242157455891100
3.024-3.1450.32231370.239357355872100
3.145-3.2880.30031420.231857575899100
3.288-3.46130.28231400.189557715911100
3.4613-3.67790.25021460.173857715917100
3.6779-3.96160.27071450.16258115956100
3.9616-4.35970.20631440.13858055949100
4.3597-4.98930.2061400.125658435983100
4.9893-6.2810.2471390.155659186057100
6.281-37.01520.21761510.153361436294100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0788-0.39890.13871.24970.00251.4522-0.10070.1039-0.16910.0890.1605-0.15030.09430.0607-0.07130.2820.00820.04150.3159-0.05140.3884-10.734465.2643-19.3852
20.8324-0.48090.45520.923-0.15680.962-0.03540.12330.05380.03820.1064-0.1829-0.11460.2412-0.06220.3256-0.02430.06340.3966-0.07510.3866-7.469768.5619-19.6593
30.78870.42740.54652.09540.00891.5091-0.11150.11030.06040.19340.0625-0.3522-0.53620.2682-0.05660.3959-0.058-0.01450.3598-0.04960.4054-7.610582.1557-15.7546
41.94211.10190.80761.9411-1.05372.54580.1291-0.0963-0.20830.6308-0.1484-0.7311-0.31320.5-0.08630.4831-0.1103-0.08360.4351-0.09860.4996-1.068283.0451-5.4036
51.17560.19380.48761.5025-0.4381.2299-0.0589-0.140.01360.4080.1134-0.2001-0.20860.1878-0.07050.45040.0447-0.06260.391-0.0410.3369-7.007975.8484-4.3272
61.19860.0787-0.16971.3688-0.36430.4321-0.19380.03030.1685-0.00710.16710.054-0.3113-0.3353-0.04340.52530.02990.01830.33550.04040.406-25.003586.9807-30.0419
70.204-0.2396-0.06311.86950.55950.3337-0.28110.2559-0.2572-0.74450.0760.1186-0.1421-0.04820.11030.9307-0.23750.01540.6486-0.01180.3925-21.112268.6075-57.9685
81.0729-1.0071-0.33433.12930.12771.7054-0.22850.287-0.0522-0.3470.22-0.1031-0.15770.2738-0.04010.6028-0.17480.12820.5532-0.03530.4164-11.333778.3202-44.6626
92.06560.02360.07670.27730.35771.5056-0.0760.09210.29890.0530.1876-0.3932-0.46540.1148-0.00920.6762-0.10350.030.29770.01910.3638-13.362787.5393-29.8525
100.34160.15630.04031.1973-0.41541.4163-0.08910.19110.0339-0.18620.1441-0.0177-0.2064-0.2545-0.1090.3155-0.04270.01870.36190.02190.3449-21.913477.3818-35.4961
110.7328-0.5606-0.03840.80460.60741.03050.08680.10310.3586-0.12990.12280.8768-0.4585-0.1965-0.23450.57780.17510.02510.46510.08660.5848-33.618890.022-27.2727
123.56590.5135-0.84921.40330.15771.01960.5149-0.2987-0.3038-0.2829-0.08650.0680.0695-0.0152-0.28690.496-0.13710.00830.4391-0.00440.3544-23.25560.6707-37.6063
130.87420.0542-0.24361.3256-0.3860.3868-0.03550.32760.0196-0.47520.23290.5431-0.1344-0.5928-0.10030.4884-0.0352-0.11960.63410.09530.5032-40.602774.9995-39.1339
141.3880.0014-0.36581.5118-0.23851.6395-0.05560.0750.1332-0.09810.20.2994-0.5303-0.3876-0.15940.43360.04530.01250.5210.09890.4176-36.309484.4046-37.4281
151.0297-0.1665-0.19121.37950.40771.21860.04070.01590.0495-0.0544-0.0421-0.32720.01890.0871-0.02510.2576-0.0314-0.0580.43120.05180.4513-57.775739.0908-1.4849
160.5720.1754-0.84481.5836-0.38241.3948-0.0577-0.19430.00970.30430.0269-0.30570.16370.2720.06670.4158-0.0328-0.16660.48040.05460.4916-57.044431.45658.4746
171.0455-0.6108-0.22720.38960.10982.374-0.0896-0.18180.04150.43660.1546-0.45990.69520.2579-0.05150.74810.1616-0.16460.56780.0890.5771-51.630218.531911.5299
180.5959-0.0178-0.21141.43320.01281.9881-0.0502-0.0355-0.03250.05360.0555-0.37010.31430.26840.0180.40070.0689-0.07680.42090.01630.511-52.852821.12950.5427
190.5041-0.1795-0.05881.24950.11471.3673-0.0978-0.21130.1720.4664-0.0015-0.1964-0.2948-0.12410.0880.5641-0.0203-0.15590.5369-0.05610.40623.753758.770820.0811
200.84110.70330.09371.76110.34940.084-0.0398-0.3-0.03230.6772-0.0728-0.3276-0.18290.16980.1140.57870.0285-0.22010.609-0.01260.40879.812747.705925.0015
210.56580.06770.0340.94570.41620.4798-0.0706-0.22750.03720.4041-0.0781-0.236-0.04080.03760.16410.531-0.0203-0.12040.47980.04270.34074.733944.054818.4251
221.25230.2271-0.02531.1695-0.08620.00530.1087-0.1344-0.17440.44520.0226-0.05980.1947-0.3127-0.07260.5385-0.09830.04780.6162-0.01240.3739-9.758833.297323.2718
232.48070.85061.00030.54710.17440.51320.1598-0.02010.0046-0.247-0.21790.03350.041-0.1561-0.01320.4998-0.0306-0.11540.47130.02560.3960.448457.33232.8469
241.55640.06630.61750.9336-0.68061.4215-0.1098-0.23770.07090.3477-0.04920.4508-0.4053-0.50740.10530.40650.08260.03730.675-0.05580.4284-16.992151.350116.0174
250.7810.0235-0.03521.62150.15091.67540.0389-0.29920.03160.663-0.06140.17080.1314-0.4430.02320.497-0.07060.03450.7418-0.04210.3561-12.699345.278823.3775
261.32210.34890.05111.4641-0.00791.6711-0.39220.2059-0.1855-0.26440.27740.12110.33190.12260.15320.8174-0.1197-0.01220.367-0.05210.5547-46.647813.2148-39.4196
270.61620.6787-0.13231.7159-0.02831.2682-0.16160.0805-0.3049-0.41410.179-0.13190.54080.10940.03920.63970.01770.05770.3565-0.06160.5468-43.123813.303-35.4447
282.6818-1.2536-0.01560.6232-0.04780.534-0.1015-0.62570.9046-0.00260.1801-0.0461-0.02830.0409-0.08250.43450.0850.02290.392-0.05010.5578-46.942524.1913-20.2318
290.5148-0.1589-0.50920.9271-0.02880.72630.0646-0.228-0.0023-0.47230.11040.59330.2618-0.5217-0.06570.4761-0.1228-0.11930.54180.01390.7266-66.163820.9228-33.9212
300.9787-0.30170.43571.32730.17191.4938-0.15990.1735-0.2633-0.39420.12090.43390.7039-0.35960.03790.7206-0.1784-0.05910.43630.00370.633-60.962711.1589-36.3951
311.00050.7532-0.40971.4711-0.31710.7947-0.41530.14660.0244-0.39580.3135-0.0129-0.31120.2687-0.1410.4941-0.0552-0.08280.4031-0.05340.4396-36.701239.5448-39.093
321.07361.0924-0.26791.2881-0.39471.4171-0.114-0.2284-0.2261-0.0493-0.1367-0.32910.00930.53330.1910.30170.0385-0.02260.53030.00330.5267-24.72138.7556-27.2939
331.15360.40290.01251.6784-0.39471.0012-0.21140.0357-0.0249-0.49520.2222-0.00950.0540.06260.050.4172-0.0616-0.03070.3518-0.03280.417-40.444736.2173-39.6271
341.20090.16380.50331.11110.43773.5819-0.4003-0.0779-0.736-0.3830.0747-0.61130.47180.64830.07670.55910.10480.04870.5697-0.08710.798-22.103623.3212-38.9614
354.72110.08161.46761.17480.42992.5968-0.55710.5925-0.4684-1.27610.3396-0.4845-0.07120.12420.11231.1742-0.21780.30580.5479-0.07090.6084-27.154331.6831-59.1038
361.78470.0851-1.14142.08370.15930.7522-0.2120.42110.15-0.69960.0718-0.382-0.18930.49130.08130.7878-0.20770.13310.6192-0.11710.4118-24.769540.501-55.5482
371.05790.4421-0.22121.375-0.39231.0401-0.32350.27070.0968-0.62420.1906-0.1313-0.00250.11180.10580.6177-0.1499-0.00470.444-0.02520.3944-30.483545.0044-50.2965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 185 )A9 - 185
2X-RAY DIFFRACTION2chain 'A' and (resid 186 through 232 )A186 - 232
3X-RAY DIFFRACTION3chain 'A' and (resid 233 through 296 )A233 - 296
4X-RAY DIFFRACTION4chain 'A' and (resid 297 through 323 )A297 - 323
5X-RAY DIFFRACTION5chain 'A' and (resid 324 through 395 )A324 - 395
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 41 )B9 - 41
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 79 )B42 - 79
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 123 )B80 - 123
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 160 )B124 - 160
10X-RAY DIFFRACTION10chain 'B' and (resid 161 through 232 )B161 - 232
11X-RAY DIFFRACTION11chain 'B' and (resid 233 through 252 )B233 - 252
12X-RAY DIFFRACTION12chain 'B' and (resid 253 through 276 )B253 - 276
13X-RAY DIFFRACTION13chain 'B' and (resid 277 through 343 )B277 - 343
14X-RAY DIFFRACTION14chain 'B' and (resid 344 through 395 )B344 - 395
15X-RAY DIFFRACTION15chain 'C' and (resid 9 through 232 )C9 - 232
16X-RAY DIFFRACTION16chain 'C' and (resid 233 through 276 )C233 - 276
17X-RAY DIFFRACTION17chain 'C' and (resid 277 through 312 )C277 - 312
18X-RAY DIFFRACTION18chain 'C' and (resid 313 through 395 )C313 - 395
19X-RAY DIFFRACTION19chain 'D' and (resid 9 through 96 )D9 - 96
20X-RAY DIFFRACTION20chain 'D' and (resid 97 through 123 )D97 - 123
21X-RAY DIFFRACTION21chain 'D' and (resid 124 through 231 )D124 - 231
22X-RAY DIFFRACTION22chain 'D' and (resid 232 through 252 )D232 - 252
23X-RAY DIFFRACTION23chain 'D' and (resid 253 through 276 )D253 - 276
24X-RAY DIFFRACTION24chain 'D' and (resid 277 through 343 )D277 - 343
25X-RAY DIFFRACTION25chain 'D' and (resid 344 through 395 )D344 - 395
26X-RAY DIFFRACTION26chain 'E' and (resid 9 through 49 )E9 - 49
27X-RAY DIFFRACTION27chain 'E' and (resid 50 through 252 )E50 - 252
28X-RAY DIFFRACTION28chain 'E' and (resid 253 through 276 )E253 - 276
29X-RAY DIFFRACTION29chain 'E' and (resid 277 through 312 )E277 - 312
30X-RAY DIFFRACTION30chain 'E' and (resid 313 through 395 )E313 - 395
31X-RAY DIFFRACTION31chain 'F' and (resid 9 through 49 )F9 - 49
32X-RAY DIFFRACTION32chain 'F' and (resid 50 through 123 )F50 - 123
33X-RAY DIFFRACTION33chain 'F' and (resid 124 through 252 )F124 - 252
34X-RAY DIFFRACTION34chain 'F' and (resid 253 through 276 )F253 - 276
35X-RAY DIFFRACTION35chain 'F' and (resid 277 through 296 )F277 - 296
36X-RAY DIFFRACTION36chain 'F' and (resid 297 through 322 )F297 - 322
37X-RAY DIFFRACTION37chain 'F' and (resid 323 through 395 )F323 - 395

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