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- PDB-5uco: Benzophenone synthase from Hypericum androsaemum -

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Basic information

Entry
Database: PDB / ID: 5uco
TitleBenzophenone synthase from Hypericum androsaemum
Components2,4,6-trihydroxybenzophenone synthase
KeywordsTRANSFERASE / thiolase / polyketide / benzoyl-CoA
Function / homology
Function and homology information


2,3',4,6-tetrahydroxybenzophenone synthase / 2,4,6-trihydroxybenzophenone synthase / tetrahydroxybenzophenone synthase activity / trihydroxybenzophenone synthase activity / benzoyl-CoA metabolic process / malonyl-CoA metabolic process / polyketide biosynthetic process / acyltransferase activity
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,4,6-trihydroxybenzophenone synthase
Similarity search - Component
Biological speciesHypericum androsaemum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 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 22, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,0362
Polymers86,0362
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-18 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.890, 121.780, 184.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 2,4,6-trihydroxybenzophenone synthase / 2 / 3' / 4 / 6-tetrahydroxybenzophenone synthase / Benzophenone synthase / HaBPS


Mass: 43017.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: codon optimized for E.coli expression, His-tag removed after purification
Source: (gene. exp.) Hypericum androsaemum (plant) / Gene: BPS / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8SAS8, 2,3',4,6-tetrahydroxybenzophenone synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Reservoir: PIPES (pH 6.5) 100mM, PEG8000 18%; 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: Apr 5, 2013 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→184.97 Å / Num. all: 18840 / Num. obs: 18840 / % possible obs: 85 % / Redundancy: 3.5 % / Biso Wilson estimate: 21.7 Å2 / Rpim(I) all: 0.142 / Rrim(I) all: 0.294 / Rsym value: 0.253 / Net I/av σ(I): 2.2 / Net I/σ(I): 4.5 / Num. measured all: 65535
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.85-32.40.4981.4185.5
3-3.192.40.3731.9184.1
3.19-3.412.40.2942.3184.2
3.41-3.682.40.2113.2183
3.68-4.032.40.1684183.4
4.03-4.514.30.3051.8182.2
4.51-5.24.50.232.6181.6
5.2-6.374.90.2482.4182.5
6.37-9.017.30.2622.41100
9.01-46.2426.90.1753.2199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BI5

1bi5


Resolution: 2.85→46.242 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.09
RfactorNum. reflection% reflection
Rfree0.2589 1881 10 %
Rwork0.2011 --
obs0.207 18809 84.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.38 Å2 / Biso mean: 15.6359 Å2 / Biso min: 2.58 Å2
Refinement stepCycle: final / Resolution: 2.85→46.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5748 0 0 45 5793
Biso mean---10.34 -
Num. residues----754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035858
X-RAY DIFFRACTIONf_angle_d0.6517926
X-RAY DIFFRACTIONf_chiral_restr0.027898
X-RAY DIFFRACTIONf_plane_restr0.0031032
X-RAY DIFFRACTIONf_dihedral_angle_d12.0152130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.9270.32971440.24591290143485
2.927-3.01320.36231400.25141270141085
3.0132-3.11040.28941430.24821279142284
3.1104-3.22150.29591410.23271274141583
3.2215-3.35050.3081400.22121258139883
3.3505-3.50290.28381420.21331280142283
3.5029-3.68750.24051400.20391265140583
3.6875-3.91850.25511410.19011258139983
3.9185-4.22080.23841400.17971261140182
4.2208-4.64520.21191390.15931261140081
4.6452-5.31650.21651400.16381250139081
5.3165-6.6950.26621480.20951344149285
6.695-46.24860.21051830.18316381821100

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