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- PDB-3oit: Crystal structure of curcuminoid synthase CUS from Oryza sativa -

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Basic information

Entry
Database: PDB / ID: 3oit
TitleCrystal structure of curcuminoid synthase CUS from Oryza sativa
ComponentsOs07g0271500 protein
KeywordsTRANSFERASE / type III polyketide synthases
Function / homology
Function and homology information


bisdemethoxycurcumin synthase / bisdemethoxycurcumin synthase activity / flavonoid biosynthetic process / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / identical protein binding
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
Bisdemethoxycurcumin synthase
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMiyazono, K. / Um, J. / Imai, F.L. / Katsuyama, Y. / Ohnishi, Y. / Horinouchi, S. / Tanokura, M.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of curcuminoid synthase CUS from Oryza sativa
Authors: Miyazono, K. / Um, J. / Imai, F.L. / Katsuyama, Y. / Ohnishi, Y. / Horinouchi, S. / Tanokura, M.
History
DepositionAug 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Os07g0271500 protein
B: Os07g0271500 protein


Theoretical massNumber of molelcules
Total (without water)83,6112
Polymers83,6112
Non-polymers00
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-10 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.780, 68.510, 211.720
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 Os07g0271500 protein / CUS / curcuminoid synthase / chalcone synthase


Mass: 41805.637 Da / Num. of mol.: 2 / Fragment: UNP residues 17-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Strain: subsp. japonica / Gene: OJ1001_C01.122, OSJNBb0002J01.6, Os07g0271500 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LIL0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCDNA WITH ACCESSION NUMBER AK109558 WAS USED FOR THE PRODUCTION OF PROTEIN CUS. AND AUTHOR STATED ...CDNA WITH ACCESSION NUMBER AK109558 WAS USED FOR THE PRODUCTION OF PROTEIN CUS. AND AUTHOR STATED RESIDUE 46 SHOULD BE ILE IN THE SEQUENCE OF AK109558.

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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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM Tris-HCl, 20% PEG 4000, 200mM NaCl, 6% 1,6-hexanediol, pH 8.5, 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: Feb 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 57647 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.965 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.050.2870.485.140967419941990.507100
2.05-2.110.2120.3836.539963409940980.404100
2.11-2.170.2060.3327.339002400240010.35100
2.17-2.240.1850.2848.438140391939140.399.9
2.24-2.310.1810.259.336562377137560.26499.6
2.31-2.390.1460.20610.935208363036230.21799.8
2.39-2.480.130.17612.234286353735250.18599.7
2.48-2.580.10.13714.632632338633740.14599.6
2.58-2.70.0850.12315.831413326232510.1399.7
2.7-2.830.070.10517.230005313631270.11199.7
2.83-2.980.0590.08818.728807301830080.09399.7
2.98-3.160.0410.0722.726494279227860.07499.8
3.16-3.380.0270.05427.725346269626960.057100
3.38-3.650.0210.04632.322861249324930.049100
3.65-40.0190.04333.920577227622720.04699.8
4-4.470.0150.0526133701213021300.054100
4.47-5.160.0140.04771.928732185818570.04999.9
5.16-6.320.0150.04964.624705160016000.051100
6.32-8.940.0110.03887.617852127012700.04100
8.94-200.0080.026125.168327516670.02788.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BI5

1bi5


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.808 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 2921 5.1 %RANDOM
Rwork0.1952 ---
obs0.1968 54728 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.16 Å2 / Biso mean: 36.755 Å2 / Biso min: 16.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å20 Å20 Å2
2---0.17 Å20 Å2
3----2.46 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5598 0 0 438 6036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225703
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9687737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.865734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02323.11254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8915917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9071555
X-RAY DIFFRACTIONr_chiral_restr0.0850.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214359
X-RAY DIFFRACTIONr_mcbond_it0.5241.53663
X-RAY DIFFRACTIONr_mcangle_it1.01425841
X-RAY DIFFRACTIONr_scbond_it1.72732040
X-RAY DIFFRACTIONr_scangle_it2.8614.51896
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 240 -
Rwork0.288 3958 -
all-4198 -
obs--100 %
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)
10.57090.08460.01820.89780.34921.40660.0303-0.0997-0.06490.1058-0.051-0.0670.13820.02390.02070.02380.0023-0.0140.05940.01380.0544-4.59248.4587-14.989
20.5739-0.0872-0.07590.8486-0.03611.03730.02290.06450.0133-0.2282-0.03970.1168-0.0505-0.13510.01680.0670.0235-0.03720.0379-0.01680.0266-13.84417.0347-42.0415
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 399
2X-RAY DIFFRACTION2B20 - 398

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