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- PDB-7dex: Crystal Structures of Anthocyanin 5,3'-aromatic acyltransferase H... -

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Basic information

Entry
Database: PDB / ID: 7dex
TitleCrystal Structures of Anthocyanin 5,3'-aromatic acyltransferase H174A mutant with caffeoyl-CoA
ComponentsAnthocyanin 5-aromatic acyltransferase
KeywordsTRANSFERASE / acyltransferase / anthocyanin / plant enzyme / delphinidin / caffeoyl-CoA
Function / homologyanthocyanin 5-(6'''-hydroxycinnamoyltransferase) / anthocyanin 5-(6'''-hydroxycinnamoyltransferase) activity / : / : / Chloramphenicol acetyltransferase-like domain superfamily / cytoplasm / Chem-H5L / Anthocyanin 5-aromatic acyltransferase
Function and homology information
Biological speciesGentiana triflora (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2702
Polymers52,3401
Non-polymers9301
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint3 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.858, 117.894, 184.058
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: 52339.984 Da / Num. of mol.: 1 / Mutation: H174A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gentiana triflora (plant) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ZWR8, anthocyanin 5-(6'''-hydroxycinnamoyltransferase)
#2: Chemical ChemComp-H5L / S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (E)-3-[3,4-bis(oxidanyl)phenyl]prop-2-enethioate / Caffeoyl-CoA


Mass: 929.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H42N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 54.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Hepes, sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→29.65 Å / Num. obs: 19939 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 51.12 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 1.107 / Num. unique obs: 2826

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E1U

2e1u


Resolution: 2.5→29.65 Å / SU ML: 0.3628 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.7564 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2561 964 4.84 %
Rwork0.1931 18973 -
obs0.1962 19937 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.34 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3640 0 60 71 3771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933793
X-RAY DIFFRACTIONf_angle_d1.1765154
X-RAY DIFFRACTIONf_chiral_restr0.0551577
X-RAY DIFFRACTIONf_plane_restr0.006650
X-RAY DIFFRACTIONf_dihedral_angle_d15.53132307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.35421180.30472648X-RAY DIFFRACTION99.1
2.63-2.80.2941480.26622679X-RAY DIFFRACTION100
2.8-3.020.32341510.25292651X-RAY DIFFRACTION100
3.02-3.320.31261310.22892690X-RAY DIFFRACTION100
3.32-3.80.23651360.18082703X-RAY DIFFRACTION99.96
3.8-4.780.21151310.1522753X-RAY DIFFRACTION100
4.78-29.650.23751490.17282849X-RAY DIFFRACTION99.87

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