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

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Basic information

Entry
Database: PDB / ID: 6dxc
TitleCrystal structure of chalcone synthase from Selaginella moellendorffii - S340C mutant
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: 1.54 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


Theoretical massNumber of molelcules
Total (without water)84,0832
Polymers84,0832
Non-polymers00
Water15,871881
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-10 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.220, 66.380, 103.000
Angle α, β, γ (deg.)90.000, 91.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chalcone synthase


Mass: 42041.430 Da / Num. of mol.: 2 / Mutation: S340C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selaginella moellendorffii (plant) / Gene: SELMODRAFT_271225 / Plasmid: pHis8-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D8S128
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 881 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
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

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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: 1.54→31.589 Å / Num. obs: 105252 / % possible obs: 95.55 % / Redundancy: 1.8 % / Biso Wilson estimate: 10.9 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.04892 / Rpim(I) all: 0.04892 / Rrim(I) all: 0.06919 / Net I/σ(I): 9.66
Reflection shellResolution: 1.54→1.595 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.1642 / Mean I/σ(I) obs: 3.06 / Num. unique obs: 8805 / CC1/2: 0.891 / Rpim(I) all: 0.1642 / Rrim(I) all: 0.2322 / % possible all: 80.52

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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: 1.54→31.589 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.29
RfactorNum. reflection% reflection
Rfree0.1725 1905 1.81 %
Rwork0.1425 --
obs0.1431 105175 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.27 Å2 / Biso mean: 17.6714 Å2 / Biso min: 3.81 Å2
Refinement stepCycle: final / Resolution: 1.54→31.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5768 0 0 881 6649
Biso mean---29.34 -
Num. residues----756
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 (%)
1.54-1.57850.25441190.19496123624279
1.5785-1.62120.18991210.17136754687588
1.6212-1.66890.20321350.15957198733394
1.6689-1.72280.20261360.15757193732993
1.7228-1.78430.19051260.15447140726693
1.7843-1.85580.19741360.15087452758897
1.8558-1.94020.20091330.167579771298
1.9402-2.04250.17751440.13687613775799
2.0425-2.17040.15981360.13667590772699
2.1704-2.33790.14861430.13117667781099
2.3379-2.57310.16561460.12587655780199
2.5731-2.94520.18071420.136377117853100
2.9452-3.70980.14271440.13647735787999
3.7098-31.59570.16931440.141578608004100
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)
10.3755-0.16830.15140.3339-0.0320.7758-0.0258-0.03940.03170.08220.0062-0.0324-0.04880.0150.03010.0668-0.0134-0.00130.0641-0.00470.084129.168923.714935.5841
20.40490.08160.10750.36770.0270.3871-0.0078-0.005-0.04130.06250.0006-0.00910.0403-0.03920.01090.06140.0057-0.0020.07390.00220.073120.424716.12329.443
30.952-0.0074-0.03640.6868-0.03730.91010.00230.0351-0.1697-0.0070.001-0.03480.1528-0.007-0.01170.09140.0058-0.00320.0657-0.00320.106526.69721.744926.6728
40.5091-0.09310.08150.57830.09560.4399-0.0105-0.08520.07370.09270.01280.0055-0.0642-0.02810.00820.061-0.00020.01080.0602-0.01470.07190.280930.224929.7328
50.3009-0.02820.02090.1433-0.20.6405-0.04150.01630.04930.01550.0284-0.0245-0.13460.03330.05160.0740.01740.00410.0605-0.01350.09478.852332.260318.7055
60.86680.15030.13250.82680.08670.8964-0.02180.070.0677-0.04150.0302-0.0014-0.0917-0.00720.01960.06990.0072-0.00150.06850.01320.07990.297736.46299.1162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 149 )A9 - 149
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 264 )A150 - 264
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 386 )A265 - 386
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 220 )B9 - 220
5X-RAY DIFFRACTION5chain 'B' and (resid 221 through 264 )B221 - 264
6X-RAY DIFFRACTION6chain 'B' and (resid 265 through 386 )B265 - 386

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