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- PDB-4kec: SbHCT-complex form -

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Basic information

Entry
Database: PDB / ID: 4kec
TitleSbHCT-complex form
ComponentsHydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase
KeywordsTRANSFERASE / Hydroxycinnamoyl transferase
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Transferase family / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4KE / COENZYME A / Uncharacterized protein
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWalker, A.M. / Hayes, R.P. / Youn, B. / Vermerris, W. / Sattler, S.E. / Kang, C.
CitationJournal: Plant Physiol. / Year: 2013
Title: Elucidation of the structure and reaction mechanism of sorghum hydroxycinnamoyltransferase and its structural relationship to other coenzyme a-dependent transferases and synthases.
Authors: Walker, A.M. / Hayes, R.P. / Youn, B. / Vermerris, W. / Sattler, S.E. / Kang, C.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9733
Polymers48,8851
Non-polymers1,0882
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.167, 137.167, 63.569
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase / Protein Sb04g025760


Mass: 48884.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: Sb04g025760, SORBIDRAFT_04g025760 / Production host: Escherichia coli (E. coli) / References: UniProt: C5XXB7
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-4KE / (3R,4S,5R)-3,4-dihydroxy-5-{[(2E)-3-(4-hydroxyphenyl)prop-2-enoyl]oxy}cyclohex-1-ene-1-carboxylic acid


Mass: 320.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.53 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES monohydrate pH 6.0, 22% v/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25964 / % possible obs: 97 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.4→2.5092 Å / % possible all: 90

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.622 Å / SU ML: 0.36 / σ(F): 1.36 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 1207 4.49 %
Rwork0.205 --
obs0.2072 25968 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6741 Å2-0 Å20 Å2
2---2.6741 Å20 Å2
3---5.3482 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 71 127 3545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113516
X-RAY DIFFRACTIONf_angle_d1.254796
X-RAY DIFFRACTIONf_dihedral_angle_d18.8191310
X-RAY DIFFRACTIONf_chiral_restr0.071511
X-RAY DIFFRACTIONf_plane_restr0.005630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.49610.33931300.26932822X-RAY DIFFRACTION100
2.4961-2.60970.34031380.25992830X-RAY DIFFRACTION100
2.6097-2.74730.31411360.25932838X-RAY DIFFRACTION100
2.7473-2.91940.31241310.25852831X-RAY DIFFRACTION100
2.9194-3.14470.31991380.24922821X-RAY DIFFRACTION100
3.1447-3.46110.2631310.22942869X-RAY DIFFRACTION100
3.4611-3.96170.261360.19692858X-RAY DIFFRACTION100
3.9617-4.99040.19651280.16452862X-RAY DIFFRACTION100
4.9904-46.63090.22251390.17532932X-RAY DIFFRACTION100

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