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- PDB-5kjt: Crystal structure of Arabidopsis thaliana HCT in complex with p-c... -

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Basic information

Entry
Database: PDB / ID: 5kjt
TitleCrystal structure of Arabidopsis thaliana HCT in complex with p-coumaroyl-CoA
ComponentsShikimate O-hydroxycinnamoyltransferase
KeywordsTRANSFERASE / phenylpropanoid metabolism / HCT / BAHD / acyltransferase
Function / homology
Function and homology information


quinate O-hydroxycinnamoyltransferase activity / shikimate O-hydroxycinnamoyltransferase / shikimate O-hydroxycinnamoyltransferase activity / positive regulation of flavonoid biosynthetic process / lignin biosynthetic process / cell wall organization / membrane / cytoplasm
Similarity search - Function
Transferase family / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
p-coumaroyl-CoA / Shikimate O-hydroxycinnamoyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLevsh, O. / Chiang, Y.C. / Tung, C.F. / Noel, J.P. / Wang, Y. / Weng, J.K.
Funding support United States, 3items
OrganizationGrant numberCountry
Pew Scholar Program in the Biomedical Sciences United States
Searle Scholars Program United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Biochemistry / Year: 2016
Title: Dynamic Conformational States Dictate Selectivity toward the Native Substrate in a Substrate-Permissive Acyltransferase.
Authors: Levsh, O. / Chiang, Y.C. / Tung, C.F. / Noel, J.P. / Wang, Y. / Weng, J.K.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shikimate O-hydroxycinnamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9402
Polymers48,0271
Non-polymers9141
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.190, 99.190, 84.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Shikimate O-hydroxycinnamoyltransferase / Hydroxycinnamoyl transferase / Hydroxycinnamoyl-Coenzyme A shikimate/quinate hydroxycinnamoyltransferase


Mass: 48026.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HST, HCT, At5g48930, K19E20.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9FI78, shikimate O-hydroxycinnamoyltransferase
#2: Chemical ChemComp-WCA / p-coumaroyl-CoA


Mass: 913.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H42N7O18P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.24
Details: 0.5 M ammonium acetate, 0.1M MOPSO-NaOH, pH 7.24, 18% PEG 8000. Substrate soaking drops consisted of 10% (v/v) 100 mM p-coumaroyl-CoA in resevoir solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979482 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979482 Å / Relative weight: 1
ReflectionResolution: 2.5→49.6 Å / Num. obs: 16893 / % possible obs: 99.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.5→49.595 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 851 5.04 %
Rwork0.1829 --
obs0.186 16888 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 59 102 3530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073529
X-RAY DIFFRACTIONf_angle_d1.6014814
X-RAY DIFFRACTIONf_dihedral_angle_d13.5111298
X-RAY DIFFRACTIONf_chiral_restr0.073524
X-RAY DIFFRACTIONf_plane_restr0.006622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.65680.36461400.25412596X-RAY DIFFRACTION98
2.6568-2.86190.29591380.23572630X-RAY DIFFRACTION99
2.8619-3.14990.29931390.22942653X-RAY DIFFRACTION100
3.1499-3.60560.26251400.20442675X-RAY DIFFRACTION100
3.6056-4.54210.21691450.15152692X-RAY DIFFRACTION100
4.5421-49.60470.19461490.14722791X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -70.8281 Å / Origin y: 129.1242 Å / Origin z: 3.6005 Å
111213212223313233
T0.3134 Å2-0.0898 Å2-0.0123 Å2-0.2734 Å2-0.0216 Å2--0.2241 Å2
L0.6232 °20.4019 °2-0.3746 °2-1.9897 °2-0.3443 °2--0.6378 °2
S0.1131 Å °-0.0736 Å °0.0089 Å °0.1534 Å °-0.0962 Å °0.031 Å °-0.036 Å °0.0591 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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