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- PDB-7x0d: Crystal structure of phospholipase A1, CaPLA1 -

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Basic information

Entry
Database: PDB / ID: 7x0d
TitleCrystal structure of phospholipase A1, CaPLA1
ComponentsPhospholipase A1
KeywordsHYDROLASE / Phospholipase A1
Function / homologyPhospholipase A1-II / phospholipase A1 activity / Fungal lipase-like domain / Lipase (class 3) / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lipid catabolic process / Alpha/Beta hydrolase fold / Phospholipase A1
Function and homology information
Biological speciesCapsicum annuum (sweet pepper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3972515576 Å
AuthorsHeo, Y. / Lee, I. / Moon, S. / Lee, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2022
Title: Crystal Structures of the Plant Phospholipase A1 Proteins Reveal a Unique Dimerization Domain.
Authors: Heo, Y. / Lee, I. / Moon, S. / Yun, J.H. / Kim, E.Y. / Park, S.Y. / Park, J.H. / Kim, W.T. / Lee, W.
History
DepositionFeb 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A1
B: Phospholipase A1
C: Phospholipase A1
D: Phospholipase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,4548
Polymers181,0704
Non-polymers3844
Water9,152508
1
A: Phospholipase A1
B: Phospholipase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7274
Polymers90,5352
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-56 kcal/mol
Surface area31110 Å2
MethodPISA
2
C: Phospholipase A1
hetero molecules

D: Phospholipase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7274
Polymers90,5352
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area2970 Å2
ΔGint-56 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.313, 59.568, 147.319
Angle α, β, γ (deg.)90.000, 90.139, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Phospholipase A1


Mass: 45267.461 Da / Num. of mol.: 4 / Mutation: Y113W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capsicum annuum (sweet pepper) / Gene: PLA1, T459_03599 / Production host: Escherichia coli (E. coli)
References: UniProt: A5YW95, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 0.2M ammonium sulfate, 10% PEG 8000, 10% 2-propanol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.0082 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0082 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 67379 / % possible obs: 96.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 26.5624458342 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 13.97
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.79 / Num. unique obs: 3305 / % possible all: 95.5

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YIJ

2yij


Resolution: 2.3972515576→49.1061888254 Å / SU ML: 0.336679155301 / Cross valid method: FREE R-VALUE / σ(F): 1.33340615603 / Phase error: 26.7039351573
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.260150206969 3409 5.06154325845 %
Rwork0.206454591431 63942 -
obs0.209146720375 67351 95.8037581258 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.5776849861 Å2
Refinement stepCycle: LAST / Resolution: 2.3972515576→49.1061888254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12411 0 20 508 12939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023726199146612769
X-RAY DIFFRACTIONf_angle_d0.54524202021417315
X-RAY DIFFRACTIONf_chiral_restr0.04212752482911848
X-RAY DIFFRACTIONf_plane_restr0.003982322785022200
X-RAY DIFFRACTIONf_dihedral_angle_d13.66801402977483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3973-2.43150.3612597808681200.2909861992832429X-RAY DIFFRACTION88.7225896276
2.4315-2.46780.3449385442611280.2996114864262702X-RAY DIFFRACTION96.4224872232
2.4678-2.50630.3609730594291280.2702822725052624X-RAY DIFFRACTION95.6884561892
2.5063-2.54740.3492383533331420.2701996963742632X-RAY DIFFRACTION95.8203799655
2.5474-2.59140.3340823558371330.2601199216842691X-RAY DIFFRACTION95.7937584803
2.5914-2.63850.31701681041470.2504505725732615X-RAY DIFFRACTION95.3071083506
2.6385-2.68920.2985612440191520.246173125422636X-RAY DIFFRACTION95.023858214
2.6892-2.74410.3378184963691560.2368048265182574X-RAY DIFFRACTION95.2214858737
2.7441-2.80380.3304412958881350.2423705068792639X-RAY DIFFRACTION95.2282869894
2.8038-2.8690.2914582450521450.2315064360452613X-RAY DIFFRACTION94.7115384615
2.869-2.94070.3172632385611430.2349477447242635X-RAY DIFFRACTION94.8446568795
2.9407-3.02020.276932953331430.2298071315872601X-RAY DIFFRACTION94.7841105354
3.0202-3.10910.2685674153641330.229942661832657X-RAY DIFFRACTION95.4172366621
3.1091-3.20940.2501198103121520.2226440432362634X-RAY DIFFRACTION94.8586993531
3.2094-3.32410.2553640433051240.2197476824222660X-RAY DIFFRACTION95.0170648464
3.3241-3.45720.2364395329831500.2019021932572599X-RAY DIFFRACTION94.9896337249
3.4572-3.61450.2628238748641410.1990198019042650X-RAY DIFFRACTION95.5167693361
3.6145-3.8050.2670459729781570.187354950232630X-RAY DIFFRACTION94.9250681199
3.805-4.04320.2393979932221350.1796215831192675X-RAY DIFFRACTION95.9044368601
4.0432-4.35520.2177630578391430.1683342834712710X-RAY DIFFRACTION96.7774762551
4.3552-4.79320.2003594052741500.1579063941422755X-RAY DIFFRACTION98.6417657046
4.7932-5.4860.2119725553681400.1709547642532832X-RAY DIFFRACTION99.7650218194
5.486-6.90870.233887596691760.1861913193332806X-RAY DIFFRACTION99.8994974874
6.9087-49.10610.1891147250491360.1681195067722943X-RAY DIFFRACTION99.5795601552

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