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- PDB-6lpw: Structure of Spermidine disinapoyl transferases(SDT) from Arabido... -

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Basic information

Entry
Database: PDB / ID: 6lpw
TitleStructure of Spermidine disinapoyl transferases(SDT) from Arabidopsis thaliana
ComponentsSpermidine sinapoyl-CoA acyltransferase
KeywordsPLANT PROTEIN / BAHD transferase / phenolamides / spermidine / putrescine / multisite-acylation / molecular mechanism / sequence similarity network
Function / homology
Function and homology information


spermidine disinapoyl transferase / sinapoyl spermidine:sinapoyl CoA N-acyltransferase activity / spermidine:sinapoyl CoA N-acyltransferase activity / spermidine metabolic process / polyamine biosynthetic process
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
SPERMIDINE / Spermidine sinapoyl-CoA acyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 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 sinapoyl-CoA acyltransferase
B: Spermidine sinapoyl-CoA acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0113
Polymers100,8652
Non-polymers1451
Water2,234124
1
B: Spermidine sinapoyl-CoA acyltransferase
hetero molecules

A: Spermidine sinapoyl-CoA acyltransferase


Theoretical massNumber of molelcules
Total (without water)101,0113
Polymers100,8652
Non-polymers1451
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+5/2,-y,z+1/21
Buried area2720 Å2
ΔGint-1 kcal/mol
Surface area36140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.989, 103.062, 135.411
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 sinapoyl-CoA acyltransferase / Spermidine disinapoyl transferase


Mass: 50432.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SDT / Production host: Escherichia coli (E. coli)
References: UniProt: O80467, spermidine disinapoyl transferase
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


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


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES (pH 6.5), 25% W/V PEG 4000 at 20 C

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 500K / Detector: PIXEL / Date: Jan 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 32701 / % possible obs: 95.82 % / Redundancy: 3 % / CC1/2: 0.09 / Net I/σ(I): 15
Reflection shellResolution: 2.49→2.49 Å / CC1/2: 0.09

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G0B

4g0b


Resolution: 2.401→48.161 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.98
RfactorNum. reflection% reflection
Rfree0.2444 1661 5.09 %
Rwork0.1998 --
obs0.2021 32617 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.22 Å2 / Biso mean: 41.4353 Å2 / Biso min: 15.77 Å2
Refinement stepCycle: final / Resolution: 2.401→48.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6786 0 10 124 6920
Biso mean--43.51 40.3 -
Num. residues----867
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.41-2.47120.28861190.2167236689
2.4712-2.5510.29411360.2145244992
2.551-2.64220.27261330.2099246593
2.6422-2.74790.28691330.2124248593
2.7479-2.8730.26921330.2205249293
2.873-3.02440.3011430.2181250094
3.0244-3.21390.26581470.2127257596
3.2139-3.4620.24271260.2019265199
3.462-3.81020.21111290.1924270199
3.8102-4.36130.2411490.1762268699
4.3613-5.49350.20241420.18342748100
5.4935-5.49350.23641710.2108283899

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