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- PDB-3ov2: Curcumin synthase 1 from Curcuma longa -

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Basic information

Entry
Database: PDB / ID: 3ov2
TitleCurcumin synthase 1 from Curcuma longa
ComponentsCurcumin synthase
KeywordsTRANSFERASE / type III polyketide synthase
Function / homology
Function and homology information


curcumin synthase / curcumin synthase activity / flavonoid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
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
MALONATE ION / Curcumin synthase 1
Similarity search - Component
Biological speciesCurcuma longa (turmeric)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsKatsuyama, Y. / Miyazono, K. / Tanokura, M. / Ohnishi, Y. / Horinouchi, S.
CitationJournal: To be Published
Title: A hydrophobic cavity discovered in a curcumin synthase facilitates utilization of a beta-keto acid as an extender substrate for the atypical type III polyleteide synthase
Authors: Katsuyama, Y. / Miyazono, K. / Tanokura, M. / Ohnishi, Y. / Horinouchi, S.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Curcumin synthase
B: Curcumin synthase
C: Curcumin synthase
D: Curcumin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,89581
Polymers174,5564
Non-polymers5,33977
Water9,728540
1
A: Curcumin synthase
B: Curcumin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,43147
Polymers87,2782
Non-polymers3,15345
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-13 kcal/mol
Surface area28050 Å2
MethodPISA
2
C: Curcumin synthase
D: Curcumin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,46434
Polymers87,2782
Non-polymers2,18632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-16 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.180, 115.810, 221.240
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
Curcumin synthase /


Mass: 43638.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Curcuma longa (turmeric) / Gene: CURS1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: C0SVZ6
#2: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 63 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3M sodium malonate pH 7.0, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.32 Å / Num. obs: 165495 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.405 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.35
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.32-2.380.6050.4212.63588012236122330.517100
2.38-2.450.5120.36333520211987119860.446100
2.45-2.520.4830.3443.13424011626116240.422100
2.52-2.590.4240.3013.63330511279112780.369100
2.59-2.680.3510.264.13236310958109570.319100
2.68-2.770.3170.2314.73138110590105900.283100
2.77-2.880.2650.1975.33035410249102470.242100
2.88-30.2080.1646.328983980498020.202100
3-3.130.1790.1417.127747942094190.173100
3.13-3.280.140.1128.826335899189910.137100
3.28-3.460.1080.0910.624991859085900.11100
3.46-3.670.0840.07412.323498814681450.091100
3.67-3.920.0660.06214.521581757975770.076100
3.92-4.240.0610.05815.520076710971030.07299.9
4.24-4.640.0520.0511718464653165260.06399.9
4.64-5.190.0480.04817.216618587058600.05999.8
5.19-5.990.0560.05415.814996520552040.067100
5.99-7.340.0560.05816.512649439643910.07199.9
7.34-10.380.0420.04920.19700337533700.0699.9
10.380.0330.03921.54620186616020.04885.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→19.82 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.744 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 4333 5 %RANDOM
Rwork0.1835 ---
obs0.1861 86427 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.54 Å2 / Biso mean: 28.5862 Å2 / Biso min: 8.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.32→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12153 0 350 540 13043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212684
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.97417017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82451555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4723.345562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08152126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.24915104
X-RAY DIFFRACTIONr_chiral_restr0.0830.21847
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219544
X-RAY DIFFRACTIONr_mcbond_it0.5321.57735
X-RAY DIFFRACTIONr_mcangle_it1.018212383
X-RAY DIFFRACTIONr_scbond_it1.72234949
X-RAY DIFFRACTIONr_scangle_it2.9014.54634
LS refinement shellResolution: 2.32→2.379 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 322 -
Rwork0.201 5878 -
all-6200 -
obs--99.98 %
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)
10.41850.00460.12260.4647-0.0430.1711-0.04630.0007-0.03690.01120.0555-0.0126-0.0093-0.0611-0.00920.0109-0.0096-0.00910.06520.00190.049719.5293-18.0942-52.5361
20.42-0.33040.23370.46-0.15810.1472-0.1177-0.07870.0350.0960.1158-0.0999-0.0375-0.04120.00190.09790.0292-0.02820.0509-0.02590.033738.637-25.9385-29.8916
30.3957-0.070.04020.2201-0.08430.29470.01950.0102-0.01250.0006-0.01580.0321-0.0617-0.0014-0.00370.01980.01530.0010.05180.02590.062811.57523.0765-23.0535
40.35520.17460.10060.5462-0.00550.29250.02560.05780.00870.1222-0.00860.00740.06360.0153-0.0170.0481-0.00030.00140.04530.0230.021116.82452.2629-0.9389
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 391
2X-RAY DIFFRACTION2B3 - 391
3X-RAY DIFFRACTION3C2 - 393
4X-RAY DIFFRACTION4D3 - 391

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