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- PDB-6dx9: Crystal structure of chalcone synthase from Equisetum arvense -

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Basic information

Entry
Database: PDB / ID: 6dx9
TitleCrystal structure of chalcone synthase from Equisetum arvense
ComponentsChalcone synthase
KeywordsTRANSFERASE / Thiolase / Flavonoid / Polyketide synthase
Function / homology
Function and homology information


chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process
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 speciesEquisetum arvense (field horsetail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsWeng, J.K. / Liou, G. / Chiang, Y.C. / Wang, Y.
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

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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)88,6022
Polymers88,6022
Non-polymers00
Water12,809711
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-11 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.954, 112.764, 130.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chalcone synthase / / Naringenin-chalcone synthase


Mass: 44300.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equisetum arvense (field horsetail) / Gene: CHS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9MBB1, chalcone synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.15 M LiCl, 8% PEG 6000, and 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2015
RadiationMonochromator: single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→65.401 Å / Num. obs: 125911 / % possible obs: 99.97 % / Redundancy: 9.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1013 / Rpim(I) all: 0.03516 / Rrim(I) all: 0.1074 / Net I/σ(I): 13.26
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.58 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 12431 / CC1/2: 0.697 / Rpim(I) all: 0.546 / Rrim(I) all: 1.673 / % possible all: 99.9

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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: 1.5→65.401 Å / FOM work R set: 0.896 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1781 6224 4.94 %
Rwork0.1582 119672 -
obs0.1591 125896 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.28 Å2 / Biso mean: 20.79 Å2 / Biso min: 9.62 Å2
Refinement stepCycle: final / Resolution: 1.5→65.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6003 0 0 711 6714
Biso mean---30.24 -
Num. residues----783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096181
X-RAY DIFFRACTIONf_angle_d1.2628370
X-RAY DIFFRACTIONf_chiral_restr0.052937
X-RAY DIFFRACTIONf_plane_restr0.0071087
X-RAY DIFFRACTIONf_dihedral_angle_d12.3892299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.5170.48312100.454939544164
1.517-1.53490.42911920.391139334125
1.5349-1.55360.35471990.367539344133
1.5536-1.57330.35372100.306739434153
1.5733-1.5940.28412000.272939294129
1.594-1.61580.2791930.24739684161
1.6158-1.63890.23172070.212939374144
1.6389-1.66340.23432320.199439554187
1.6634-1.68940.20341840.186939474131
1.6894-1.71710.22162140.173139674181
1.7171-1.74670.19852020.161339354137
1.7467-1.77840.16772160.152739554171
1.7784-1.81270.16451950.147339544149
1.8127-1.84970.16771980.149839864184
1.8497-1.88990.18582010.143839854186
1.8899-1.93380.15752040.138939414145
1.9338-1.98220.15521970.139440114208
1.9822-2.03580.15142190.145439604179
2.0358-2.09570.14741970.141139704167
2.0957-2.16340.14911990.129439834182
2.1634-2.24070.16672120.125139904202
2.2407-2.33040.16262200.13639774197
2.3304-2.43650.22060.14640234229
2.4365-2.56490.18172000.150740104210
2.5649-2.72560.15372070.144540074214
2.7256-2.93610.15062310.142840304261
2.9361-3.23150.15171880.146440454233
3.2315-3.69910.16552270.140940604287
3.6991-4.66030.15122280.142740984326
4.6603-65.46370.19632360.179242854521
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)
10.78330.28730.56270.88560.46582.87480.0531-0.1018-0.00480.201-0.0381-0.0651-0.00970.0422-0.02060.17540.00760.00870.09450.01510.12765.3086-5.58334.8598
20.2310.30320.41321.72190.75880.91190.0383-0.0305-0.01330.11140.012-0.16460.05220.0941-0.06050.11830.0171-0.00620.15810.00870.160511.28360.8611.5113
30.26080.04730.07680.67550.16340.3799-0.0014-0.0114-0.0231-0.001-0.016-0.02640.08420.00970.01770.13080.00630.01330.13780.00190.12180.3636-0.6903-9.2936
40.7309-0.1344-0.1751.36710.40041.1493-0.00360.0148-0.09730.0569-0.03120.10820.2174-0.10240.03120.1928-0.02660.02040.12970.00340.1314-8.4724-16.8651-6.6583
50.4350.34140.26060.64830.17420.790.0035-0.02430.0165-0.0119-0.02190.0383-0.0088-0.02210.01830.08040.01540.00220.1286-0.00990.1316-6.448827.6578-10.5838
60.1507-0.01370.03390.42750.08160.4754-0.01650.01590.0038-0.0795-0.0060.00650.0161-0.00650.01760.1168-0.00250.00220.1371-0.00080.1254-5.878713.9278-16.3991
71.3360.05940.00481.1876-0.10991.1390.00140.15570.0036-0.3198-0.0162-0.02830.0623-0.01470.02330.1888-0.00290.00960.12240.01070.0971-2.997820.5499-33.4511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 67 )A14 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 123 )A68 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 275 )A124 - 275
4X-RAY DIFFRACTION4chain 'A' and (resid 276 through 405 )A276 - 405
5X-RAY DIFFRACTION5chain 'B' and (resid 14 through 123 )B14 - 123
6X-RAY DIFFRACTION6chain 'B' and (resid 124 through 275 )B124 - 275
7X-RAY DIFFRACTION7chain 'B' and (resid 276 through 404 )B276 - 404

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