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- PDB-6dxa: Crystal structure of chalcone synthase from Pinus sylvestris -

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Basic information

Entry
Database: PDB / ID: 6dxa
TitleCrystal structure of chalcone synthase from Pinus sylvestris
ComponentsChalcone synthase
KeywordsTRANSFERASE / Thiolase / Flavonoid / Polyketide synthase
Function / homology
Function and homology information


: / chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process / polyketide biosynthetic process
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / 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 ...Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / 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 speciesPinus sylvestris (Scots pine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 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)86,7562
Polymers86,7562
Non-polymers00
Water12,322684
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-17 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.017, 100.059, 65.882
Angle α, β, γ (deg.)90.000, 110.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chalcone synthase / Naringenin-chalcone synthase


Mass: 43377.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pinus sylvestris (Scots pine) / Gene: CHS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30079, chalcone synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.14 M NH4Cl, 20% (v/v) PEG 3350, and 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2014
RadiationMonochromator: single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.01→61.585 Å / Num. obs: 46489 / % possible obs: 99.31 % / Redundancy: 3.6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.1424 / Rpim(I) all: 0.08803 / Rrim(I) all: 0.1679 / Net I/σ(I): 10.4
Reflection shellResolution: 2.01→2.082 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.6168 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 4596 / CC1/2: 0.76 / Rpim(I) all: 0.4357 / Rrim(I) all: 0.7584 / % possible all: 98.75

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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: 2.01→61.585 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.86
RfactorNum. reflection% reflection
Rfree0.2196 2348 5.05 %
Rwork0.1576 --
obs0.1607 46458 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.31 Å2 / Biso mean: 17.9 Å2 / Biso min: 1.1 Å2
Refinement stepCycle: final / Resolution: 2.01→61.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6005 0 0 684 6689
Biso mean---23.94 -
Num. residues----783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126123
X-RAY DIFFRACTIONf_angle_d1.2978281
X-RAY DIFFRACTIONf_chiral_restr0.05937
X-RAY DIFFRACTIONf_plane_restr0.0071067
X-RAY DIFFRACTIONf_dihedral_angle_d14.022291
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.0510.29021390.232525562695100
2.051-2.09560.33331470.25592558270598
2.0956-2.14440.26011120.188726522764100
2.1444-2.1980.24791450.170625792724100
2.198-2.25740.30671300.22262463259395
2.2574-2.32390.28291460.175526082754100
2.3239-2.39890.23551250.167126052730100
2.3989-2.48460.21141460.152225812727100
2.4846-2.58410.23191390.150626162755100
2.5841-2.70170.20971170.1562629274699
2.7017-2.84420.22691540.148626072761100
2.8442-3.02240.19591630.1525732736100
3.0224-3.25570.19331390.141526292768100
3.2557-3.58330.17821320.13662586271899
3.5833-4.10170.1941320.13352583271598
4.1017-5.16730.171350.115326222757100
5.1673-61.61420.19961470.15852663281099
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)
10.4741-0.00670.01741.1691-0.54681.26070.0959-0.0779-0.00550.1324-0.0460.11730.0369-0.0550.01260.06720.0090.01540.0654-0.00440.083264.3925-11.067325.7393
21.7370.7035-0.43221.4159-0.15971.346-0.15330.26710.1048-0.2430.1624-0.0762-0.16780.1911-0.01640.1999-0.04840.01110.19420.04460.088475.75159.0654-16.5707
30.40610.04690.05490.33890.09670.5585-0.02410.04010.0817-0.04820.00780.0371-0.0690.02420.00350.07560.0050.0060.07110.01830.100270.10368.04278.8704
40.2693-0.12650.20850.4282-0.03320.22050.00510.05960.0104-0.0530.03450.00570.02870.0532-0.00850.05460.00140.02010.06040.00410.083771.177-5.014215.3547
50.46590.4198-0.32880.4237-0.31970.5094-0.03950.0954-0.0568-0.12490.0031-0.01950.0940.15530.08190.10680.01420.01980.15650.00670.104577.18843.1199-3.7418
60.2446-0.01060.31740.72850.2430.44-0.05970.1616-0.1206-0.15120.0786-0.06590.02870.0742-0.01190.0868-0.00510.01790.1292-0.01920.039775.0828-9.0667.3136
70.49450.2893-0.40571.0042-0.23320.82590.00430.1054-0.0644-0.09380.0462-0.04610.10110.0072-0.01060.11220.0289-0.02550.1031-0.02770.088770.9349-20.6287-2.2056
80.55920.6322-0.42161.1799-0.10810.94580.11340.10240.0942-0.07570.00460.16730.0812-0.085-0.08510.11280.03430.0010.08990.0220.08161.7034-6.5612-0.5728
90.97660.22570.18770.42020.12810.4380.03320.1-0.2305-0.10220.0124-0.01480.1275-0.061-0.01010.0908-0.0112-0.03420.062-0.01590.076963.9527-16.70084.7826
100.25790.02090.18980.3843-0.07380.7513-0.03370.00570.0469-0.0121-0.0193-0.11-0.11820.18610.02650.07550.00820.02140.1008-0.00870.105894.56134.653924.6093
110.21110.4242-0.26182.5595-1.34870.9184-0.09230.0999-0.085-0.14670.0759-0.2230.03670.08150.08030.0644-0.01980.03850.1009-0.02360.089995.719-5.226518.1826
120.5278-0.11440.09290.2766-0.0080.62370.05750.1876-0.0726-0.01650.0302-0.00730.0170.2007-0.03690.05580.0572-0.00410.121-0.040.1388.1079-12.394915.4492
130.3167-0.13350.16390.0567-0.07460.3158-0.01130.01440.06510.0350.033-0.0214-0.01360.0806-0.01910.0641-0.01070.02250.0793-0.00770.083686.2651-0.221323.7815
140.6991-0.2822-0.01251.16920.34390.38790.0244-0.3411-0.07820.18240.076-0.03290.1695-0.10270.11230.10750.01470.00270.0508-0.00540.085679.9474-15.075934.1579
150.747-0.2139-0.20.27060.45371.2387-0.09840.03120.1577-0.06960.0956-0.0422-0.19330.0792-0.14930.1071-0.00820.00530.047-0.0050.125981.362815.503222.8894
160.62960.0888-0.15720.4658-0.06770.8117-0.041-0.10320.05860.08750.04040.0091-0.00490.01490.00110.09560.0009-0.00060.0688-0.00460.07284.26671.042641.2844
170.612-0.18530.56090.9341-0.57891.17510.0543-0.0277-0.00070.0596-0.0451-0.13860.05950.0082-0.03960.04850.00750.00530.0629-0.00820.079782.3213-6.06940.2089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 34 )A4 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 66 )A35 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 159 )A67 - 159
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 201 )A160 - 201
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 230 )A202 - 230
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 275 )A231 - 275
7X-RAY DIFFRACTION7chain 'A' and (resid 276 through 329 )A276 - 329
8X-RAY DIFFRACTION8chain 'A' and (resid 330 through 360 )A330 - 360
9X-RAY DIFFRACTION9chain 'A' and (resid 361 through 394 )A361 - 394
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 95 )B3 - 95
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 122 )B96 - 122
12X-RAY DIFFRACTION12chain 'B' and (resid 123 through 159 )B123 - 159
13X-RAY DIFFRACTION13chain 'B' and (resid 160 through 230 )B160 - 230
14X-RAY DIFFRACTION14chain 'B' and (resid 231 through 251 )B231 - 251
15X-RAY DIFFRACTION15chain 'B' and (resid 252 through 275 )B252 - 275
16X-RAY DIFFRACTION16chain 'B' and (resid 276 through 360 )B276 - 360
17X-RAY DIFFRACTION17chain 'B' and (resid 361 through 394 )B361 - 394

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