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- PDB-5uc5: Chalcone synthase from Malus domestica -

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Basic information

Entry
Database: PDB / ID: 5uc5
TitleChalcone synthase from Malus domestica
ComponentsCHS2 chalcone synthase
KeywordsTRANSFERASE / thiolase / polyketide
Function / homology
Function and homology information


chalcone synthase / naringenin-chalcone synthase activity / 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
CHS2 chalcone synthase
Similarity search - Component
Biological speciesMalus domestica (apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.102 Å
AuthorsStewart Jr, C.E. / Noel, J.P.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Molecular architectures of benzoic acid-specific type III polyketide synthases.
Authors: Stewart, C. / Woods, K. / Macias, G. / Allan, A.C. / Hellens, R.P. / Noel, J.P.
History
DepositionDec 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: CHS2 chalcone synthase
B: CHS2 chalcone synthase


Theoretical massNumber of molelcules
Total (without water)85,5162
Polymers85,5162
Non-polymers00
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-18 kcal/mol
Surface area27470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.819, 56.628, 111.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsDimer as determined by gel filtration

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Components

#1: Protein CHS2 chalcone synthase


Mass: 42758.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malus domestica (apple) / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K9MUA0, chalcone synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Reservoir: Sodium-MOPSO (pH 7.0) 100mM, Ammonium Acetate 300mM, PEG8000 14%. Ratio of protein to reservoir= 1:1

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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 315r / Detector: CCD / Date: Dec 5, 2009 / Details: mirrors
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: 2.1→50 Å / Num. obs: 42128 / % possible obs: 94.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 32.64 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.144.80.496194.8
2.14-2.184.80.431194.8
2.18-2.224.90.391193.8
2.22-2.264.70.387193.9
2.26-2.314.90.328193.9
2.31-2.374.80.292193.5
2.37-2.424.90.257193.6
2.42-2.494.80.22193.1
2.49-2.564.80.193193.2
2.56-2.654.90.182192.5
2.65-2.744.80.163192.8
2.74-2.854.80.145192.2
2.85-2.984.80.13193
2.98-3.144.70.117193
3.14-3.334.60.107194.9
3.33-3.594.60.101196.4
3.59-3.954.50.089197.9
3.95-4.524.60.069199.3
4.52-5.750.054199.9
5.7-5050.044199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.22data extraction
HKLdata scaling
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BI5

1bi5


Resolution: 2.102→40.99 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.58
RfactorNum. reflection% reflection
Rfree0.2092 2126 5.05 %
Rwork0.1658 --
obs0.168 42079 94.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.31 Å2 / Biso mean: 41.9287 Å2 / Biso min: 16.05 Å2
Refinement stepCycle: final / Resolution: 2.102→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5960 0 0 346 6306
Biso mean---41.14 -
Num. residues----774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036139
X-RAY DIFFRACTIONf_angle_d0.7438327
X-RAY DIFFRACTIONf_chiral_restr0.027957
X-RAY DIFFRACTIONf_plane_restr0.0031072
X-RAY DIFFRACTIONf_dihedral_angle_d13.0542311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1022-2.15110.29561500.21892410256088
2.1511-2.20490.23071660.21322614278094
2.2049-2.26460.24761590.20242593275294
2.2646-2.33120.27861380.20042602274094
2.3312-2.40640.22791190.20162615273493
2.4064-2.49240.25351150.18752624273993
2.4924-2.59220.241300.17942610274093
2.5922-2.71010.25231580.18582565272392
2.7101-2.8530.24371340.18942600273493
2.853-3.03170.19721150.19382623273893
3.0317-3.26570.26831250.1812662278794
3.2657-3.59420.19741380.16732750288896
3.5942-4.11380.17581390.14582813295298
4.1138-5.18130.15251660.123128673033100
5.1813-40.99790.20481740.151230053179100
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)
12.34540.3227-1.55670.73150.4122.05240.26690.55220.3506-0.311-0.14360.1575-0.3848-0.0778-0.04420.41170.1229-0.06410.68590.07480.30980.226313.560912.5736
21.0602-0.3524-0.2340.5489-0.27662.4747-0.06010.1668-0.18950.0832-0.02090.15710.111-0.16360.07810.2646-0.00410.01030.2457-0.06320.346476.355-1.935239.102
31.7741-0.70420.25911.716-0.45451.6353-0.0490.12490.20380.21020.01080.1284-0.1874-0.17840.04610.30240.04970.03560.25950.00410.320775.34716.895539.3625
41.6659-0.47860.96081.7695-0.32481.30460.03990.17280.11330.0944-0.08530.2504-0.0425-0.22390.02290.30310.07840.01460.3448-0.00090.341268.060516.108232.5516
54.5672-1.2619-0.76331.24790.51430.58550.26431.12810.6255-0.2043-0.2422-0.0027-0.4282-0.35610.01130.43710.09380.02260.52790.16710.397487.822321.32917.42
62.3359-0.0237-0.56351.8235-0.57961.3531-0.1652-0.0187-0.70770.0123-0.0414-0.19190.26030.1560.17430.27320.01870.03080.2256-0.01280.4187112.3-13.928334.9451
71.4539-0.01240.11144.8435-2.46262.7256-0.0204-0.0136-0.02450.386-0.1565-0.4214-0.20320.20410.21280.25820.006-0.00090.1762-0.00470.246104.15976.898835.4745
82.2955-0.8117-0.26441.419-0.55611.13260.05440.2923-0.0606-0.0671-0.04380.03990.0564-0.0541-0.01840.2301-0.002-0.01260.2013-0.01670.19697.00885.55429.4461
91.6742-0.4149-0.23970.69570.1451.63920.04390.725-0.2685-0.1858-0.09130.05970.097-0.02710.03840.31230.0396-0.00710.5212-0.12280.28999.3213-3.331813.8338
104.83623.0506-2.76665.2293-3.40455.95340.10210.7872-0.33410.3542-0.0439-0.5387-0.0192-0.0486-0.00030.26470.0422-0.04230.4052-0.02490.268109.15816.010416.7501
111.38150.0403-0.26391.58440.32661.36820.12170.78330.0051-0.2802-0.1239-0.094-0.11160.10460.0530.32950.0820.00220.68-0.01440.2299101.35744.80019.4095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )A2 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 225 )A26 - 225
3X-RAY DIFFRACTION3chain 'A' and (resid 226 through 337 )A226 - 337
4X-RAY DIFFRACTION4chain 'A' and (resid 338 through 388 )A338 - 388
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 25 )B2 - 25
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 90 )B26 - 90
7X-RAY DIFFRACTION7chain 'B' and (resid 91 through 117 )B91 - 117
8X-RAY DIFFRACTION8chain 'B' and (resid 118 through 225 )B118 - 225
9X-RAY DIFFRACTION9chain 'B' and (resid 226 through 337 )B226 - 337
10X-RAY DIFFRACTION10chain 'B' and (resid 338 through 355 )B338 - 355
11X-RAY DIFFRACTION11chain 'B' and (resid 356 through 388 )B356 - 388

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