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- PDB-7dev: Crystal Structures of Anthocyanin 5,3'-aromatic acyltransferase f... -

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Basic information

Entry
Database: PDB / ID: 7dev
TitleCrystal Structures of Anthocyanin 5,3'-aromatic acyltransferase from Gentiana triflora
ComponentsAnthocyanin 5-aromatic acyltransferase
KeywordsTRANSFERASE / acyltransferase / anthocyanin / plant enzyme / delphinidin / caffeoyl-CoA
Function / homologyanthocyanin 5-(6'''-hydroxycinnamoyltransferase) / anthocyanin 5-(6'''-hydroxycinnamoyltransferase) activity / : / Transferase family / Chloramphenicol acetyltransferase-like domain superfamily / cytoplasm / Anthocyanin 5-aromatic acyltransferase
Function and homology information
Biological speciesGentiana triflora (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Shirouzu, M.
CitationJournal: Phytochemistry / Year: 2021
Title: Anthocyanin 5,3'-aromatic acyltransferase from Gentiana triflora, a structural insight into biosynthesis of a blue anthocyanin.
Authors: Murayama, K. / Kato-Murayama, M. / Sato, T. / Hosaka, T. / Ishiguro, K. / Mizuno, T. / Kitao, K. / Honma, T. / Yokoyama, S. / Tanaka, Y. / Shirouzu, M.
History
DepositionNov 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anthocyanin 5-aromatic acyltransferase


Theoretical massNumber of molelcules
Total (without water)53,4211
Polymers53,4211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19920 Å2
Unit cell
Length a, b, c (Å)51.439, 112.992, 183.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Anthocyanin 5-aromatic acyltransferase / 5AT


Mass: 53421.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gentiana triflora (plant) / Production host: Baculovirus expression vector pCTdual
References: UniProt: Q9ZWR8, anthocyanin 5-(6'''-hydroxycinnamoyltransferase)

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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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: sodium citrate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 10164 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 40.78 Å2 / Rsym value: 0.229 / Net I/σ(I): 10.47
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 991 / Rsym value: 0.777

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E1U

2e1u


Resolution: 3.1→49.54 Å / SU ML: 0.3738 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8398 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2507 1014 9.99 %
Rwork0.1908 9138 -
obs0.1967 10152 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.68 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 0 0 3602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00853692
X-RAY DIFFRACTIONf_angle_d1.04455008
X-RAY DIFFRACTIONf_chiral_restr0.0513562
X-RAY DIFFRACTIONf_plane_restr0.0072636
X-RAY DIFFRACTIONf_dihedral_angle_d13.39292208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.260.31531400.25311268X-RAY DIFFRACTION99.09
3.26-3.460.27741430.2361292X-RAY DIFFRACTION100
3.46-3.730.28561430.1991276X-RAY DIFFRACTION99.93
3.73-4.110.23181430.17721283X-RAY DIFFRACTION99.86
4.11-4.70.22941450.15871313X-RAY DIFFRACTION100
4.7-5.920.20051450.16991311X-RAY DIFFRACTION100
5.92-49.540.25591550.18991395X-RAY DIFFRACTION99.42

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