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- PDB-4yjy: Crystal structure of Type III polyketide synthase from Oryza sativa -

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Basic information

Entry
Database: PDB / ID: 4yjy
TitleCrystal structure of Type III polyketide synthase from Oryza sativa
ComponentsChalcone synthase 1
KeywordsTRANSFERASE / 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 speciesOryza sativa subsp. indica (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsWongsantichon, J. / Robinson, R.C. / Yew, W.S.
CitationJournal: Acs Catalysis / Year: 2015
Title: Synthetic Polyketide Enzymology: Platform for Biosynthesis of Antimicrobial Polyketides
Authors: Go, M.K. / Wongsantichon, J. / Cheung, V.W.N. / Chow, J.Y. / Robinson, R.C. / Yew, W.S.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chalcone synthase 1
B: Chalcone synthase 1


Theoretical massNumber of molelcules
Total (without water)86,5772
Polymers86,5772
Non-polymers00
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-14 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.420, 99.728, 169.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chalcone synthase 1 / / Polyketide synthase / OsCHS1 / Naregenin-chalcone synthase


Mass: 43288.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Gene: CHS1, CHS, OsI_035120 / Production host: Escherichia coli (E. coli) / References: UniProt: A2ZEX7, chalcone synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.1 M Tris-HCl, 2 M ammonium sulfate / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. obs: 92381 / % possible obs: 99.9 % / Redundancy: 5.7 % / Net I/σ(I): 5.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→28.889 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.54 / Phase error: 17.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1856 4601 5 %
Rwork0.1588 --
obs0.1602 92109 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→28.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5985 0 0 464 6449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076136
X-RAY DIFFRACTIONf_angle_d1.0568313
X-RAY DIFFRACTIONf_dihedral_angle_d13.7122286
X-RAY DIFFRACTIONf_chiral_restr0.044934
X-RAY DIFFRACTIONf_plane_restr0.0051088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8597-1.88080.27261300.20712652X-RAY DIFFRACTION92
1.8808-1.90290.18291330.18332938X-RAY DIFFRACTION100
1.9029-1.92610.20281490.17372867X-RAY DIFFRACTION100
1.9261-1.95050.18151710.1612876X-RAY DIFFRACTION100
1.9505-1.97620.18831470.15412910X-RAY DIFFRACTION100
1.9762-2.00320.17521440.15732881X-RAY DIFFRACTION100
2.0032-2.03180.19391530.16342889X-RAY DIFFRACTION100
2.0318-2.06220.20551490.15892883X-RAY DIFFRACTION100
2.0622-2.09440.19221390.15382947X-RAY DIFFRACTION100
2.0944-2.12870.22021690.15112876X-RAY DIFFRACTION100
2.1287-2.16540.2011580.14852886X-RAY DIFFRACTION100
2.1654-2.20480.17861690.14872894X-RAY DIFFRACTION100
2.2048-2.24710.20211330.14852900X-RAY DIFFRACTION100
2.2471-2.2930.17051420.15242923X-RAY DIFFRACTION100
2.293-2.34280.18781770.15452868X-RAY DIFFRACTION100
2.3428-2.39730.20151540.162916X-RAY DIFFRACTION100
2.3973-2.45720.19971360.16292910X-RAY DIFFRACTION100
2.4572-2.52360.1971520.16132935X-RAY DIFFRACTION100
2.5236-2.59780.20181350.16772933X-RAY DIFFRACTION100
2.5978-2.68160.21711520.17422939X-RAY DIFFRACTION100
2.6816-2.77740.21541580.17672902X-RAY DIFFRACTION100
2.7774-2.88850.19191370.17512932X-RAY DIFFRACTION100
2.8885-3.01980.20171540.18072949X-RAY DIFFRACTION100
3.0198-3.17890.18641510.17122937X-RAY DIFFRACTION100
3.1789-3.37780.19211890.16562920X-RAY DIFFRACTION100
3.3778-3.63810.18551670.15662949X-RAY DIFFRACTION100
3.6381-4.00340.16781420.14472985X-RAY DIFFRACTION100
4.0034-4.58070.1581710.1332985X-RAY DIFFRACTION100
4.5807-5.76360.16721770.14532978X-RAY DIFFRACTION99
5.7636-28.89230.18021630.173148X-RAY DIFFRACTION99
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)
10.45950.07770.01011.256-0.02481.0970.00110.0456-0.0211-0.3672-0.00410.1079-0.0023-0.0454-0.01350.19280.0202-0.03610.1673-0.00880.16860.112326.86452.9282
20.63270.1519-0.09511.09960.1241.14070.0725-0.08780.12470.0338-0.06050.1221-0.2962-0.01820.00020.1960.00660.01780.2185-0.01820.21880.830346.237275.8617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 393)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 393)

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