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- PDB-4ke4: Elucidation of the structure and reaction mechanism of Sorghum bi... -

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Basic information

Entry
Database: PDB / ID: 4ke4
TitleElucidation of the structure and reaction mechanism of Sorghum bicolor hydroxycinnamoyltransferase and its structural relationship to other CoA-dependent transferases and synthases
ComponentsHydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase
KeywordsTRANSFERASE / hydroxycinnamoyl transferase
Function / homology: / Transferase family / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.012 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 15, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,5595
Polymers48,8851
Non-polymers6754
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.947, 135.947, 64.039
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 3.49 Å3/Da / Density % sol: 64.8 %
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: Sep 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→50 Å / Num. obs: 44714 / % possible obs: 99.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.0835 Å / % possible all: 94

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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: 2.012→44.5 Å / SU ML: 0.22 / σ(F): 0.2 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 1954 4.45 %RANDOM
Rwork0.1825 ---
obs0.1836 43938 97.69 %-
all-43938 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.044 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5871 Å2-0 Å2-0 Å2
2--1.5871 Å2-0 Å2
3----3.1742 Å2
Refinement stepCycle: LAST / Resolution: 2.012→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 45 334 3743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073496
X-RAY DIFFRACTIONf_angle_d1.0124742
X-RAY DIFFRACTIONf_dihedral_angle_d13.1841289
X-RAY DIFFRACTIONf_chiral_restr0.069508
X-RAY DIFFRACTIONf_plane_restr0.005627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.012-2.08350.25681850.2174002X-RAY DIFFRACTION94
2.0835-2.16690.24151910.20584051X-RAY DIFFRACTION95
2.1669-2.26550.22091910.20324062X-RAY DIFFRACTION95
2.2655-2.38490.23251930.20084171X-RAY DIFFRACTION97
2.3849-2.53440.24911950.20234195X-RAY DIFFRACTION98
2.5344-2.730.21761910.19634221X-RAY DIFFRACTION99
2.73-3.00470.2521980.20194278X-RAY DIFFRACTION99
3.0047-3.43930.21412030.18634284X-RAY DIFFRACTION100
3.4393-4.33260.15491960.15684321X-RAY DIFFRACTION100
4.3326-44.50.17412110.15764399X-RAY DIFFRACTION100

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