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- PDB-3tvq: Crystal structure of TCM Aro/Cyc complexed with trans-dihidroquercetin -

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Basic information

Entry
Database: PDB / ID: 3tvq
TitleCrystal structure of TCM Aro/Cyc complexed with trans-dihidroquercetin
ComponentsMultifunctional cyclase-dehydratase-3-O-methyl transferase tcmN
KeywordsTRANSFERASE / TETRACENOMYCIN / AROMATASE / CYCLASE / TAXIFOLIN / DIHYROQUERCETIN / Helix-grip fold / MULTIFUNCTIONAL CYCLASE-DEHYDRATASE-3-O-METHYL TRANSFERASE
Function / homology
Function and homology information


tetracenomycin F2 synthase / O-methyltransferase activity / antibiotic biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
Coenzyme Q-binding protein COQ10, START domain / Polyketide cyclase / dehydrase and lipid transport / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / Winged helix DNA-binding domain superfamily ...Coenzyme Q-binding protein COQ10, START domain / Polyketide cyclase / dehydrase and lipid transport / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DQH / Tetracenomycin biosynthesis bifunctional cyclase/O-methyl transferase TcmN
Similarity search - Component
Biological speciesStreptomyces glaucescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsAmes, B.D. / Lee, M.-Y. / Tsai, S.-C.
CitationJournal: Biochemistry / Year: 2012
Title: Insight into the Molecular Basis of Aromatic Polyketide Cyclization: Crystal Structure and in Vitro Characterization of WhiE-ORFVI.
Authors: Lee, M.Y. / Ames, B.D. / Tsai, S.C.
History
DepositionSep 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Multifunctional cyclase-dehydratase-3-O-methyl transferase tcmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8472
Polymers19,5431
Non-polymers3041
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.455, 105.011, 51.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Multifunctional cyclase-dehydratase-3-O-methyl transferase tcmN


Mass: 19542.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces glaucescens (bacteria) / Gene: tcmN / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16559
#2: Chemical ChemComp-DQH / (2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE / (2R,3R)-TRANS-DIHYDROQUERCETIN


Mass: 304.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% PEG 8000, 0.1M SODIUM ACETATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0332
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 20, 2005
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.67→31.52 Å / Num. obs: 22482 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 21.8 Å2
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 5.9 % / % possible all: 100

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AIL

1ail


Resolution: 1.67→31.52 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3415 -RANDOM
Rwork0.208 ---
obs0.208 22482 97.8 %-
all-23020 --
Displacement parametersBiso mean: 24.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.67→31.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1245 0 22 154 1421
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.67→1.75 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.277 361 -
Rwork0.256 --
obs--92.3 %

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