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- PDB-6dxf: Crystal structure of chalcone synthase from Selaginella moellendo... -

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Basic information

Entry
Database: PDB / ID: 6dxf
TitleCrystal structure of chalcone synthase from Selaginella moellendorffii - hydrogen peroxide treated
ComponentsChalcone synthase
KeywordsTRANSFERASE / Thiolase / Flavonoid / Polyketide synthase
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
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 speciesSelaginella moellendorffii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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 13, 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


Theoretical massNumber of molelcules
Total (without water)84,0192
Polymers84,0192
Non-polymers00
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-11 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.540, 67.064, 102.993
Angle α, β, γ (deg.)90.000, 91.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chalcone synthase


Mass: 42009.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selaginella moellendorffii (plant) / Gene: SELMODRAFT_271225 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D8S128
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1 M MOPSO (pH 6.6), 0.3 M Mg(NO3)2, 19% (v/v) PEG 4000, and 5 mM DTT. H2O2 soaking was performed by adding hydrogen peroxide to 1 mM to the cryoprotection solution (17% glycerol and 83% ...Details: 0.1 M MOPSO (pH 6.6), 0.3 M Mg(NO3)2, 19% (v/v) PEG 4000, and 5 mM DTT. H2O2 soaking was performed by adding hydrogen peroxide to 1 mM to the cryoprotection solution (17% glycerol and 83% reservoir solution) and incubating at 277 K for 75 min

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2015
RadiationMonochromator: single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.55→102.947 Å / Num. obs: 108309 / % possible obs: 98.71 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08912 / Rpim(I) all: 0.05381 / Rrim(I) all: 0.1046 / Net I/σ(I): 11.08
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 10712 / CC1/2: 0.532 / Rpim(I) all: 0.5135 / Rrim(I) all: 0.977 / % possible all: 98.24

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→102.947 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.48
RfactorNum. reflection% reflection
Rfree0.1825 5408 4.99 %
Rwork0.1532 --
obs0.1547 108286 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.23 Å2 / Biso mean: 24.03 Å2 / Biso min: 10.05 Å2
Refinement stepCycle: final / Resolution: 1.55→102.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 0 686 6458
Biso mean---33.43 -
Num. residues----757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015925
X-RAY DIFFRACTIONf_angle_d1.2468036
X-RAY DIFFRACTIONf_chiral_restr0.05926
X-RAY DIFFRACTIONf_plane_restr0.0071035
X-RAY DIFFRACTIONf_dihedral_angle_d13.1752206
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 (%)
1.55-1.56760.33561670.28913377354498
1.5676-1.58610.28971900.2763417360798
1.5861-1.60540.29421470.273408355599
1.6054-1.62570.25161940.24853394358899
1.6257-1.64710.26281920.25573414360699
1.6471-1.66970.26961690.24633473364299
1.6697-1.69350.28611420.24533428357099
1.6935-1.71880.26182060.25013392359899
1.7188-1.74570.29661900.24543421361199
1.7457-1.77430.27931760.22883399357598
1.7743-1.80490.26471670.22333417358498
1.8049-1.83770.21622050.20813378358399
1.8377-1.87310.2311730.18763375354898
1.8731-1.91130.17741980.16753423362198
1.9113-1.95290.20981720.15393408358099
1.9529-1.99830.18722020.14793437363999
1.9983-2.04830.16371700.14433458362899
2.0483-2.10370.1611860.14353450363699
2.1037-2.16560.19271780.13933462364099
2.1656-2.23550.18391760.13013484366099
2.2355-2.31540.18421700.13483410358099
2.3154-2.40810.16351810.13573391357298
2.4081-2.51770.16231890.13063438362799
2.5177-2.65050.17371810.13313444362599
2.6505-2.81650.1511860.141434763662100
2.8165-3.0340.16361900.14423452364299
3.034-3.33930.18091590.13943475363499
3.3393-3.82260.1731740.13023434360898
3.8226-4.81610.11891810.11043461364298
4.8161-103.17440.16411970.14483482367997
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)
11.1035-0.03160.45070.43160.03464.58120.01540.1614-0.0696-0.1704-0.00920.0864-0.0592-0.3361-0.03660.17340.0028-0.03310.1301-0.03060.1838101.2185-13.3004113.9973
21.55450.2782-0.23023.15460.90164.226-0.05470.1537-0.102-0.3219-0.02170.10830.1211-0.08670.07630.17740.0077-0.04230.2016-0.04450.1647101.7118-18.0247106.619
39.1656-0.4477-3.09544.2170.87664.9474-0.17190.54040.4275-0.2770.08050.3846-0.061-0.14890.04960.2326-0.0022-0.08220.19720.02870.2011107.6841-1.8744104.3716
42.35341.059-3.18341.2113-2.27967.3230.07020.11640.1137-0.02740.01650.1343-0.2052-0.1881-0.12840.12110.0127-0.01320.1172-0.00970.1315104.6792-3.2527125.5589
51.56010.3461-0.1621.2983-0.20820.40080.0426-0.01480.0885-0.0547-0.01450.0943-0.1102-0-0.0540.1320.0126-0.00110.1579-0.0130.1378110.2119-1.7595134.9873
60.66420.00660.47170.27310.05071.10690.02220.0921-0.0886-0.08740.00550.00790.01440.0625-0.03130.14830.002-0.00750.1642-0.01790.139112.2764-12.6416125.1794
70.807-0.1929-0.19551.1023-0.01530.9729-0.0585-0.0545-0.1693-0.06260.01220.07630.17310.04230.0420.13330.003-0.03960.1653-0.00650.1761114.9886-20.5746131.6225
80.8958-0.1297-0.09015.7548-2.17131.73530.04220.1904-0.3387-0.3174-0.02480.10840.23650.11260.02870.23790.0237-0.04510.2242-0.06120.2728118.8598-24.6606116.0108
91.776-0.19260.05210.8982-0.26091.30170.0255-0.0085-0.44590.0126-0.0040.10450.1595-0.011-0.02910.1521-0.0072-0.01330.1174-0.01180.2539106.286-29.0519129.6915
100.93890.5401-0.40793.0586-2.08412.17610.00710.10760.1435-0.1606-0.0652-0.0871-0.08030.14250.06050.1485-0.01720.0090.15570.00150.1152139.75316.4321123.4792
111.89630.45741.2861.9967-0.05172.1329-0.09350.25320.1822-0.18920.07880.0418-0.22260.1291-0.01010.1877-0.01690.04210.17720.05270.1637137.190111.9916116.678
122.2674-1.89673.16392.4374-3.73936.38050.11440.2201-0.0052-0.2269-0.1161-0.01130.22810.23860.08670.15890.00610.0120.1499-0.00630.132136.6856-8.7338122.95
130.74670.0484-0.03630.7418-0.16280.42710.01310.05470.0247-0.04670.00650.0525-0.050.0106-0.02810.13050.00180.00130.12940.00940.1225129.7868-7.5333129.178
140.9018-2.02350.5724.6042-1.55241.2774-0.0967-0.25-0.13210.11070.14850.07050.0076-0.008-0.06170.1293-0.00840.00510.14430.00130.1036131.7118-8.8905146.8918
150.241-0.3367-0.77121.01682.3156.4451-0.00630.07660.1358-0.2102-0.0980.1313-0.5657-0.16380.09430.25420.0098-0.00960.17530.01770.2123119.659110.3879125.3587
161.3902-1.0630.86787.6296-7.36448.285-0.0406-0.12850.02730.22950.07610.2751-0.1382-0.0697-0.09530.1484-0.00410.00550.1441-0.04690.1639123.81697.2281150.1491
171.4281-0.2877-0.25291.38250.63893.44470.03-0.07640.14560.02180.0505-0.0402-0.1682-0.0193-0.09260.145-0.01510.01210.1336-0.01030.1356135.928510.0445143.6872
181.6268-0.25060.11860.8848-0.07521.20810.0248-0.12420.0324-0.02050.0008-0.07140.01650.0665-0.0120.1517-0.01110.00460.1375-0.00420.1352136.81450.7578143.9893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 44 )A9 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 68 )A45 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 85 )A69 - 85
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 112 )A86 - 112
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 149 )A113 - 149
6X-RAY DIFFRACTION6chain 'A' and (resid 150 through 220 )A150 - 220
7X-RAY DIFFRACTION7chain 'A' and (resid 221 through 253 )A221 - 253
8X-RAY DIFFRACTION8chain 'A' and (resid 254 through 276 )A254 - 276
9X-RAY DIFFRACTION9chain 'A' and (resid 277 through 386 )A277 - 386
10X-RAY DIFFRACTION10chain 'B' and (resid 8 through 44 )B8 - 44
11X-RAY DIFFRACTION11chain 'B' and (resid 45 through 85 )B45 - 85
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 112 )B86 - 112
13X-RAY DIFFRACTION13chain 'B' and (resid 113 through 220 )B113 - 220
14X-RAY DIFFRACTION14chain 'B' and (resid 221 through 240 )B221 - 240
15X-RAY DIFFRACTION15chain 'B' and (resid 241 through 264 )B241 - 264
16X-RAY DIFFRACTION16chain 'B' and (resid 265 through 288 )B265 - 288
17X-RAY DIFFRACTION17chain 'B' and (resid 289 through 336 )B289 - 336
18X-RAY DIFFRACTION18chain 'B' and (resid 337 through 386 )B337 - 386

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