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

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Basic information

Entry
Database: PDB / ID: 5kju
TitleCrystal structure of Arabidopsis thaliana HCT in complex with p-coumaroylshikimate
ComponentsShikimate O-hydroxycinnamoyltransferase
KeywordsTRANSFERASE / phenylpropanoid metabolism / 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
Chem-6TO / Shikimate O-hydroxycinnamoyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.44 Å
AuthorsLevsh, O. / Chiang, Y.C. / Tung, C.F. / Noel, J.P. / Wang, Y. / Weng, J.K.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Pew Scholar Program in the Biomedical Sciences United States
Searle Scholars Program 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: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)48,3472
Polymers48,0271
Non-polymers3201
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.480, 99.480, 82.560
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-6TO / (3~{R},4~{S},5~{R})-3-[(~{E})-3-(4-hydroxyphenyl)prop-2-enoyl]oxy-4,5-bis(oxidanyl)cyclohexene-1-carboxylic acid


Mass: 320.294 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H16O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
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-coumaroylshikimate 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: 2.44→49.74 Å / Num. obs: 17882 / % possible obs: 99.8 % / Redundancy: 5.4 % / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.44→49.74 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.38
RfactorNum. reflection% reflection
Rfree0.2352 895 5.01 %
Rwork0.1709 --
obs0.174 17866 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.44→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 0 199 3591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093493
X-RAY DIFFRACTIONf_angle_d1.2284759
X-RAY DIFFRACTIONf_dihedral_angle_d13.6661275
X-RAY DIFFRACTIONf_chiral_restr0.046519
X-RAY DIFFRACTIONf_plane_restr0.006620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4401-2.5930.31951460.22322760X-RAY DIFFRACTION99
2.593-2.79320.30251500.20672789X-RAY DIFFRACTION100
2.7932-3.07420.2761440.20462814X-RAY DIFFRACTION100
3.0742-3.5190.25921520.18222810X-RAY DIFFRACTION100
3.519-4.43310.18751470.14322848X-RAY DIFFRACTION100
4.4331-49.75030.19811560.14382950X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -48.3255 Å / Origin y: 3.5713 Å / Origin z: -9.6258 Å
111213212223313233
T0.1715 Å20.0108 Å20.013 Å2-0.1038 Å2-0.005 Å2--0.1306 Å2
L0.2929 °2-0.248 °2-0.0344 °2-0.4326 °2-0.1697 °2--0.3974 °2
S-0.0118 Å °0.0212 Å °-0.021 Å °0.0666 Å °0.0098 Å °-0.0023 Å °-0.0461 Å °0.0181 Å °0.0003 Å °
Refinement TLS groupSelection details: all

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