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- PDB-7cys: Crystal structure of barley agmatine coumaroyltransferase (HvACT)... -

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Basic information

Entry
Database: PDB / ID: 7cys
TitleCrystal structure of barley agmatine coumaroyltransferase (HvACT), an N-acyltransferase in BAHD superfamily
ComponentsAgmatine coumaroyltransferase-1
KeywordsTRANSFERASE / acyltransferase
Function / homologyagmatine N4-coumaroyltransferase / agmatine N4-coumaroyltransferase activity / : / Transferase family / Chloramphenicol acetyltransferase-like domain superfamily / Agmatine coumaroyltransferase-1
Function and homology information
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsYamane, M. / Takenoya, M. / Sue, M. / Yajima, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of barley agmatine coumaroyltransferase, an N-acyltransferase from the BAHD superfamily.
Authors: Yamane, M. / Takenoya, M. / Yajima, S. / Sue, M.
History
DepositionSep 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agmatine coumaroyltransferase-1


Theoretical massNumber of molelcules
Total (without water)51,6281
Polymers51,6281
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.632, 59.521, 73.627
Angle α, β, γ (deg.)90.000, 91.285, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Agmatine coumaroyltransferase-1


Mass: 51628.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Gene: ACT-1, ACT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A9ZPJ6, agmatine N4-coumaroyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.08 M sodium cacodylate, pH 6.5, 0.16 M magnesium acetate, 16% (w/v) polyethylene glycol 8,000, and 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 44594 / % possible obs: 97.8 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.3
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2201 / CC1/2: 0.914 / CC star: 0.237 / % possible all: 82.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6dd2

6dd2


Resolution: 1.81→46.326 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.544 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2033 2175 4.879 %
Rwork0.1906 42403 -
all0.191 --
obs-44578 97.746 %
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: 23.607 Å2
Baniso -1Baniso -2Baniso -3
1--1.252 Å2-0 Å20.11 Å2
2--0.691 Å2-0 Å2
3---0.556 Å2
Refinement stepCycle: LAST / Resolution: 1.81→46.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 0 226 3530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133395
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173153
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.6614623
X-RAY DIFFRACTIONr_angle_other_deg1.2571.6067274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36621.118170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82815502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6641525
X-RAY DIFFRACTIONr_chiral_restr0.0950.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02741
X-RAY DIFFRACTIONr_nbd_refined0.1980.2612
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.22749
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21637
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21379
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2153
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.23
X-RAY DIFFRACTIONr_nbd_other0.1640.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0940.27
X-RAY DIFFRACTIONr_mcbond_it1.2872.41727
X-RAY DIFFRACTIONr_mcbond_other1.2872.3981726
X-RAY DIFFRACTIONr_mcangle_it2.1663.5882157
X-RAY DIFFRACTIONr_mcangle_other2.1663.5892158
X-RAY DIFFRACTIONr_scbond_it1.5872.6071668
X-RAY DIFFRACTIONr_scbond_other1.5862.6091669
X-RAY DIFFRACTIONr_scangle_it2.6093.8212466
X-RAY DIFFRACTIONr_scangle_other2.6093.8232467
X-RAY DIFFRACTIONr_lrange_it3.95328.1523613
X-RAY DIFFRACTIONr_lrange_other3.91228.073588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.8570.2391240.2432686X-RAY DIFFRACTION83.1607
1.857-1.9080.2342010.2212731X-RAY DIFFRACTION91.5964
1.908-1.9630.2231600.212998X-RAY DIFFRACTION98.5335
1.963-2.0230.2041460.192944X-RAY DIFFRACTION99.8384
2.023-2.090.2131320.1912849X-RAY DIFFRACTION99.8326
2.09-2.1630.2331340.1842753X-RAY DIFFRACTION99.9654
2.163-2.2450.2341450.1852664X-RAY DIFFRACTION99.7514
2.245-2.3360.1971240.1832550X-RAY DIFFRACTION99.6646
2.336-2.440.1971400.1852449X-RAY DIFFRACTION99.8072
2.44-2.5590.2091350.1812340X-RAY DIFFRACTION99.718
2.559-2.6970.214870.1772268X-RAY DIFFRACTION99.8728
2.697-2.8610.224950.1912110X-RAY DIFFRACTION99.6385
2.861-3.0580.1951210.1951978X-RAY DIFFRACTION99.3845
3.058-3.3020.192960.1951842X-RAY DIFFRACTION99.3846
3.302-3.6170.23760.1951707X-RAY DIFFRACTION98.7812
3.617-4.0420.185720.1921542X-RAY DIFFRACTION99.3842
4.042-4.6650.181560.1661392X-RAY DIFFRACTION99.3141
4.665-5.7080.158450.1891179X-RAY DIFFRACTION99.4314
5.708-8.0480.198570.208900X-RAY DIFFRACTION99.2739
8.048-46.3260.171290.201521X-RAY DIFFRACTION97.8648

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