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- PDB-6lpv: structure of Spermidine hydroxycinnamoyl transferases from Arabid... -

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Basic information

Entry
Database: PDB / ID: 6lpv
Titlestructure of Spermidine hydroxycinnamoyl transferases from Arabidopsis thaliana
ComponentsSpermidine hydroxycinnamoyl transferase
KeywordsPLANT PROTEIN / Key words: BAHD transferase / phenolamides / spermidine / putrescine / multisite-acylation / molecular mechanism / sequence similarity network
Function / homology
Function and homology information


spermidine:coumaroyl CoA N-acyltransferase activity / spermidine:caffeoyl CoA N-acyltransferase activity / spermidine:feruloyl CoA N-acyltransferase activity / spermidine hydroxycinnamate conjugate biosynthetic process / spermidine:sinapoyl CoA N-acyltransferase activity / pollen exine formation / N-acyltransferase activity / pollen development / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
: / Transferase family / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
COENZYME A / SPERMIDINE / Spermidine hydroxycinnamoyl transferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å
AuthorsWang, C.Y. / Zhang, P.
CitationJournal: Front Plant Sci / Year: 2020
Title: Structural and Biochemical Insights Into Two BAHD Acyltransferases ( At SHT and At SDT) Involved in Phenolamide Biosynthesis.
Authors: Wang, C. / Li, J. / Ma, M. / Lin, Z. / Hu, W. / Lin, W. / Zhang, P.
History
DepositionJan 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Spermidine hydroxycinnamoyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4053
Polymers50,4921
Non-polymers9132
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-1 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.364, 90.433, 95.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spermidine hydroxycinnamoyl transferase / BAHD-like hydroxycinnamoyl transferase


Mass: 50492.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHT / Production host: Escherichia coli (E. coli)
References: UniProt: O64470, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium sulfate, 0.1M Tris-HCl (pH 8.5), 25% W/V PEG 3350 at 20

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Data collection

DiffractionMean temperature: 81 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jan 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 22640 / % possible obs: 99.43 % / Redundancy: 2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.94
Reflection shellResolution: 2.29→2.37 Å / Num. unique obs: 22640 / CC1/2: 0.09

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G0B

4g0b


Resolution: 2.297→49.14 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 1159 5.12 %
Rwork0.2027 21479 -
obs0.2053 22638 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.55 Å2 / Biso mean: 36.6371 Å2 / Biso min: 7.63 Å2
Refinement stepCycle: final / Resolution: 2.297→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 58 133 3622
Biso mean--30.4 39.83 -
Num. residues----434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.29-2.40.32641380.2455257397
2.4012-2.52780.32781330.23382651100
2.5278-2.68620.3061460.22722629100
2.6862-2.89350.26061450.21692683100
2.8935-3.18470.27321620.21682674100
3.1847-3.64540.28121520.19932684100
3.6454-4.59230.19681500.17132711100
4.5923-50.23161330.1977287499

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