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- PDB-7cbf: Crystal structure of benzophenone synthase from Garcinia mangosta... -

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Basic information

Entry
Database: PDB / ID: 7cbf
TitleCrystal structure of benzophenone synthase from Garcinia mangostana L. pericarps reveals basis for substrate specificity and catalysis
Components2,4,6-trihydroxybenzophenone synthase
KeywordsTRANSFERASE / ACYLTRANSFERASE / BENZOPHENONE SYNTHASE / POLYKETIDE SYNTHASE / GmBPS
Function / homology
Function and homology information


2,4,6-trihydroxybenzophenone synthase / tetrahydroxybenzophenone synthase activity / trihydroxybenzophenone synthase activity / benzoyl-CoA metabolic process / malonyl-CoA metabolic process / biosynthetic process / acyltransferase activity
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-like
Similarity search - Domain/homology
IMIDAZOLE / IODIDE ION / 2,4,6-trihydroxybenzophenone synthase
Similarity search - Component
Biological speciesGarcinia mangostana (mangosteen)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsSongsiriritthigul, C. / Nualkaew, N. / Chen, C.-J.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of benzophenone synthase from Garcinia mangostana L. pericarps reveals basis for substrate specificity and catalysis.
Authors: Songsiriritthigul, C. / Nualkaew, N. / Ketudat-Cairnsb, J. / Chen, C.-J.
#1: Journal: Phytochemistry / Year: 2012
Title: Benzophenone synthase from Garcinia mangostana L. pericarps
Authors: Nualkaew, N. / Morita, H. / Shimokawa, Y. / Kinjo, K. / Kushiro, T. / De-Eknamkul, W. / Ebizuka, Y. / Abe, I.
History
DepositionJun 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,4,6-trihydroxybenzophenone synthase
B: 2,4,6-trihydroxybenzophenone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,86618
Polymers88,0902
Non-polymers1,77616
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-16 kcal/mol
Surface area26380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.810, 98.330, 112.024
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 2,4,6-trihydroxybenzophenone synthase / GmBPS


Mass: 44045.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Garcinia mangostana (mangosteen) / Gene: BPS / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS
References: UniProt: L7NCQ3, 2,4,6-trihydroxybenzophenone synthase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 46.1 % / Description: rectangular morphology
Crystal growTemperature: 291 K / Method: batch mode / pH: 6.2 / Details: 20% (w/v) PEG 3,350, 0.2 M ammonium iodide, pH 6.2

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2015
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 35272 / % possible obs: 99.5 % / Redundancy: 2.4 % / Biso Wilson estimate: 17.52 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 9.67
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.14 / Num. unique obs: 6660 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CGK

1cgk


Resolution: 2.301→24.347 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.648 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.218
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2152 1763 5.004 %
Rwork0.1697 33467 -
all0.172 --
obs-35230 99.452 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.241 Å2
Baniso -1Baniso -2Baniso -3
1--0.567 Å2-0 Å2-0 Å2
2---0.124 Å20 Å2
3---0.691 Å2
Refinement stepCycle: LAST / Resolution: 2.301→24.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 44 317 6199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136009
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175665
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.6388127
X-RAY DIFFRACTIONr_angle_other_deg1.3111.57213159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.275766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24423.077286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.829151035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5531530
X-RAY DIFFRACTIONr_chiral_restr0.0710.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021207
X-RAY DIFFRACTIONr_nbd_refined0.2060.21263
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.25334
X-RAY DIFFRACTIONr_nbtor_refined0.1550.22880
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2322
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1510.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.219
X-RAY DIFFRACTIONr_nbd_other0.1890.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.223
X-RAY DIFFRACTIONr_mcbond_it1.1221.5893049
X-RAY DIFFRACTIONr_mcbond_other1.1191.5873048
X-RAY DIFFRACTIONr_mcangle_it1.9092.3753811
X-RAY DIFFRACTIONr_mcangle_other1.912.3763812
X-RAY DIFFRACTIONr_scbond_it1.5261.8422960
X-RAY DIFFRACTIONr_scbond_other1.5251.8432961
X-RAY DIFFRACTIONr_scangle_it2.5472.664313
X-RAY DIFFRACTIONr_scangle_other2.5472.6614314
X-RAY DIFFRACTIONr_lrange_it4.14419.1446660
X-RAY DIFFRACTIONr_lrange_other4.05119.0876613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.3610.2581380.1982396X-RAY DIFFRACTION97.4615
2.361-2.4250.2241040.192391X-RAY DIFFRACTION99.9599
2.425-2.4960.251330.1752310X-RAY DIFFRACTION100
2.496-2.5720.2631270.1792258X-RAY DIFFRACTION99.8744
2.572-2.6570.2651220.1842174X-RAY DIFFRACTION99.9565
2.657-2.750.2441190.1762121X-RAY DIFFRACTION99.9554
2.75-2.8530.2161020.1682034X-RAY DIFFRACTION99.8597
2.853-2.970.238810.1632008X-RAY DIFFRACTION99.8566
2.97-3.1010.2151220.1591878X-RAY DIFFRACTION99.9001
3.101-3.2530.195920.1451815X-RAY DIFFRACTION99.8429
3.253-3.4280.188840.1511736X-RAY DIFFRACTION99.8902
3.428-3.6360.181940.1571641X-RAY DIFFRACTION99.77
3.636-3.8860.193850.1531547X-RAY DIFFRACTION99.7555
3.886-4.1960.216640.1551458X-RAY DIFFRACTION99.6726
4.196-4.5950.153730.1541320X-RAY DIFFRACTION99.1459
4.595-5.1350.209720.161211X-RAY DIFFRACTION98.5407
5.135-5.9250.191550.1971085X-RAY DIFFRACTION99.6503
5.925-7.2450.284460.208928X-RAY DIFFRACTION99.4893
7.245-10.1970.193320.167752X-RAY DIFFRACTION99.2405
10.197-24.340.254180.284402X-RAY DIFFRACTION89.7436

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