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- PDB-5kjs: Crystal Structure of Arabidopsis thaliana HCT -

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Basic information

Entry
Database: PDB / ID: 5kjs
TitleCrystal Structure of Arabidopsis thaliana HCT
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
Shikimate O-hydroxycinnamoyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.203 Å
AuthorsLevsh, O. / Chiang, Y.C. / Tung, C. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shikimate O-hydroxycinnamoyltransferase


Theoretical massNumber of molelcules
Total (without water)48,6191
Polymers48,6191
Non-polymers00
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)99.910, 99.910, 83.870
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: 48619.484 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: 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: 2.49 Å3/Da / Density % sol: 50.54 %
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

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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: 1.97→86.62 Å / Num. obs: 34427 / % possible obs: 99.9 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.203→60.222 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 2372 5.01 %
Rwork0.1798 --
obs0.1829 47321 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.203→60.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 0 199 3559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093466
X-RAY DIFFRACTIONf_angle_d1.2734720
X-RAY DIFFRACTIONf_dihedral_angle_d13.8041273
X-RAY DIFFRACTIONf_chiral_restr0.049513
X-RAY DIFFRACTIONf_plane_restr0.007617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2025-2.24750.36111440.24332614X-RAY DIFFRACTION99
2.2475-2.29640.26461420.20842633X-RAY DIFFRACTION100
2.2964-2.34980.25031300.19342654X-RAY DIFFRACTION100
2.3498-2.40850.31431420.19372661X-RAY DIFFRACTION100
2.4085-2.47370.3071360.2012631X-RAY DIFFRACTION100
2.4737-2.54640.27931380.19142674X-RAY DIFFRACTION100
2.5464-2.62860.25351360.19722659X-RAY DIFFRACTION100
2.6286-2.72260.27141380.19672648X-RAY DIFFRACTION100
2.7226-2.83160.28061400.20352636X-RAY DIFFRACTION100
2.8316-2.96050.26711460.1942635X-RAY DIFFRACTION100
2.9605-3.11650.2891420.20532663X-RAY DIFFRACTION100
3.1165-3.31180.21981360.19682635X-RAY DIFFRACTION100
3.3118-3.56750.27361430.18792646X-RAY DIFFRACTION100
3.5675-3.92640.23521400.17042634X-RAY DIFFRACTION100
3.9264-4.49440.19011390.14482646X-RAY DIFFRACTION100
4.4944-5.66180.18231430.14242627X-RAY DIFFRACTION99
5.6618-60.24420.19891370.17042653X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.6634 Å / Origin y: 43.0569 Å / Origin z: 24.1331 Å
111213212223313233
T0.3009 Å20.1056 Å20.0256 Å2-0.2401 Å2-0.0166 Å2--0.1881 Å2
L0.6339 °2-0.6393 °20.1789 °2-2.7614 °2-0.1244 °2--0.7913 °2
S0.0968 Å °0.0771 Å °0.0033 Å °-0.2993 Å °-0.0761 Å °0.0504 Å °0.0271 Å °0.058 Å °-0.0239 Å °
Refinement TLS groupSelection details: all

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