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- PDB-7pp7: Thunberia alata 16:0-ACP desaturase -

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Basic information

Entry
Database: PDB / ID: 7pp7
TitleThunberia alata 16:0-ACP desaturase
ComponentsAcyl-[acyl-carrier-protein] 6-desaturase
KeywordsOXIDOREDUCTASE / Desaturase / di-iron protein
Function / homology
Function and homology information


acyl-[acyl-carrier-protein] 6-desaturase / stearoyl-[ACP] desaturase activity / chloroplast stroma / fatty acid biosynthetic process / metal ion binding
Similarity search - Function
Fatty acid desaturase, type 2 / Fatty acid desaturase / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Acyl-[acyl-carrier-protein] 6-desaturase
Similarity search - Component
Biological speciesThunbergia alata (black-eyed Susan vine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGuy, J.E. / Whittle, E. / Cai, Y. / Chai, J. / Lindqvist, Y. / Shanklin, J.
Funding support United States, 2items
OrganizationGrant numberCountry
Swedish Research Council2011-05917 United States
Department of Energy (DOE, United States) United States
CitationJournal: Plant Physiol. / Year: 2022
Title: Regioselectivity mechanism of the Thunbergia alata Delta 6-16:0-acyl carrier protein desaturase.
Authors: Guy, J.E. / Cai, Y. / Baer, M.D. / Whittle, E. / Chai, J. / Yu, X.H. / Lindqvist, Y. / Raugei, S. / Shanklin, J.
History
DepositionSep 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-[acyl-carrier-protein] 6-desaturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5663
Polymers39,4541
Non-polymers1122
Water2,702150
1
A: Acyl-[acyl-carrier-protein] 6-desaturase
hetero molecules

A: Acyl-[acyl-carrier-protein] 6-desaturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1316
Polymers78,9082
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area5310 Å2
ΔGint-69 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.507, 76.172, 83.171
Angle α, β, γ (deg.)90.000, 102.110, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Acyl-[acyl-carrier-protein] 6-desaturase / Palmitoyl-acyl carrier protein desaturase


Mass: 39453.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct used for crystallisation was an N- terminal truncation mutant (N-delta11 construct) relative to the c-DNA sequence lacking the chloroplast transit peptide. i.e. removal of: mastithppplk
Source: (gene. exp.) Thunbergia alata (black-eyed Susan vine)
Plasmid: pET9d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: Q41510, acyl-[acyl-carrier-protein] 6-desaturase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.02 Å3/Da / Density % sol: 39.16 % / Description: Irregular shaped crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.25M CaCl2, 0.1M Tris pH 8.0 and 16% PEG 6000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.05→55.59 Å / Num. obs: 19684 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 10.2 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.135 / Net I/σ(I): 7.9
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2 / Num. unique obs: 1509 / CC1/2: 0.622 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2uw1

2uw1


Resolution: 2.05→55.59 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.861 / SU B: 6.33 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 1003 5.1 %RANDOM
Rwork0.1983 ---
obs0.2018 18680 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.75 Å2 / Biso mean: 26.306 Å2 / Biso min: 9.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å20.24 Å2
2---0.15 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 2.05→55.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 2 150 2655
Biso mean--23.08 26.34 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192615
X-RAY DIFFRACTIONr_bond_other_d0.0020.022461
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9493550
X-RAY DIFFRACTIONr_angle_other_deg1.04635674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4845324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65823.622127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16515461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.921520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212947
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02613
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 67 -
Rwork0.24 1364 -
all-1431 -
obs--99.79 %

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