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- PDB-7dtp: Crystal structure of agmatine coumaroyltransferase from Triticum ... -

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Basic information

Entry
Database: PDB / ID: 7dtp
TitleCrystal structure of agmatine coumaroyltransferase from Triticum aestivum
Componentsagmatine coumaroyltransferase
KeywordsTRANSFERASE / N-acyltransferase
Function / homology: / Transferase family / acyltransferase activity, transferring groups other than amino-acyl groups / Chloramphenicol acetyltransferase-like domain superfamily / Agmatine coumaroyltransferase-2
Function and homology information
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYamane, M. / Takenoya, M. / Sue, M. / Yajima, S.
CitationJournal: Phytochemistry / Year: 2021
Title: Molecular and structural characterization of agmatine coumaroyltransferase in Triticeae, the key regulator of hydroxycinnamic acid amide accumulation.
Authors: Yamane, M. / Takenoya, M. / Yajima, S. / Sue, M.
History
DepositionJan 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: agmatine coumaroyltransferase


Theoretical massNumber of molelcules
Total (without water)51,8771
Polymers51,8771
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17730 Å2
Unit cell
Length a, b, c (Å)63.074, 77.420, 92.122
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 agmatine coumaroyltransferase


Mass: 51876.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3B6DKZ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM MMT buffer pH 6.5, 25 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20776 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.131 / Net I/σ(I): 14.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1033 / CC1/2: 0.782 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CYS

7cys


Resolution: 2.3→48.948 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.747 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.243
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2564 1064 5.133 %
Rwork0.2331 19663 -
all0.234 --
obs-20727 99.549 %
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: 37.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.425 Å2-0 Å20 Å2
2--2.329 Å2-0 Å2
3----0.904 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 0 104 3227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133200
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173025
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.6384359
X-RAY DIFFRACTIONr_angle_other_deg1.1361.5736949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4435403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.62120.491163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46615482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7771527
X-RAY DIFFRACTIONr_chiral_restr0.050.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02747
X-RAY DIFFRACTIONr_nbd_refined0.1920.2552
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22732
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21521
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1120.25
X-RAY DIFFRACTIONr_nbd_other0.230.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.22
X-RAY DIFFRACTIONr_mcbond_it2.1393.8891627
X-RAY DIFFRACTIONr_mcbond_other2.1373.8891626
X-RAY DIFFRACTIONr_mcangle_it3.3645.8192025
X-RAY DIFFRACTIONr_mcangle_other3.3635.8192026
X-RAY DIFFRACTIONr_scbond_it2.4454.1921573
X-RAY DIFFRACTIONr_scbond_other2.4454.1931574
X-RAY DIFFRACTIONr_scangle_it4.1046.1692334
X-RAY DIFFRACTIONr_scangle_other4.1036.172335
X-RAY DIFFRACTIONr_lrange_it6.24644.7973296
X-RAY DIFFRACTIONr_lrange_other6.24644.7663292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.3540.348700.2731376X-RAY DIFFRACTION94.6335
2.354-2.4180.262720.2721395X-RAY DIFFRACTION100
2.418-2.4880.278610.281362X-RAY DIFFRACTION100
2.488-2.5650.262660.2741342X-RAY DIFFRACTION100
2.565-2.6490.324710.2651264X-RAY DIFFRACTION100
2.649-2.7410.324590.2681248X-RAY DIFFRACTION100
2.741-2.8450.254690.2451196X-RAY DIFFRACTION100
2.845-2.9610.298600.2461166X-RAY DIFFRACTION100
2.961-3.0920.295700.231109X-RAY DIFFRACTION100
3.092-3.2420.275750.2431032X-RAY DIFFRACTION100
3.242-3.4170.257560.2471026X-RAY DIFFRACTION100
3.417-3.6240.307460.233969X-RAY DIFFRACTION100
3.624-3.8730.219440.24930X-RAY DIFFRACTION100
3.873-4.1820.277510.208838X-RAY DIFFRACTION100
4.182-4.5780.216500.173784X-RAY DIFFRACTION100
4.578-5.1150.206430.187717X-RAY DIFFRACTION100
5.115-5.8990.205370.216640X-RAY DIFFRACTION100
5.899-7.2070.276260.233556X-RAY DIFFRACTION100
7.207-10.1180.156200.2447X-RAY DIFFRACTION100
10.118-48.90.254180.295266X-RAY DIFFRACTION98.6111

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