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- PDB-2yij: Crystal Structure of phospholipase A1 -

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Basic information

Entry
Database: PDB / ID: 2yij
TitleCrystal Structure of phospholipase A1
ComponentsPHOSPHOLIPASE A1-IIGAMMA
KeywordsHYDROLASE / PHOSPHOLIPASE
Function / homology
Function and homology information


diacylglycerol catabolic process / negative regulation of seed germination / monoacylglycerol catabolic process / phospholipase A1 activity / acylglycerol lipase activity / lipid storage / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / cytoplasm
Similarity search - Function
Phospholipase A1-II / Fungal lipase-like domain / Lipase (class 3) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phospholipase A1-IIgamma
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLee, I.
CitationJournal: To be Published
Title: Crystal Structure of Phospholipase A1
Authors: Lee, I.
History
DepositionMay 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A1-IIGAMMA
B: PHOSPHOLIPASE A1-IIGAMMA


Theoretical massNumber of molelcules
Total (without water)96,4602
Polymers96,4602
Non-polymers00
Water7,314406
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-21.3 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.223, 95.854, 78.891
Angle α, β, γ (deg.)90.00, 105.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHOSPHOLIPASE A1-IIGAMMA / DAD1-LIKE SEEDLING ESTABLISHMENT-RELATED LIPASE / ATDSEL / PHOSPHOLIPASE DSEL / AT4G18550 / LIPASE- ...DAD1-LIKE SEEDLING ESTABLISHMENT-RELATED LIPASE / ATDSEL / PHOSPHOLIPASE DSEL / AT4G18550 / LIPASE-LIKE PROTEIN


Mass: 48229.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)
References: UniProt: O49523, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.57 % / Description: NONE

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.979632, 0.979454, 0.971679
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9796321
20.9794541
30.9716791
ReflectionResolution: 1.7→30 Å / Num. obs: 114783 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 25.39
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.45 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→19.92 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.887 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 3.999 / ESU R Free: 4.568 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26403 67394 98.2 %RANDOM
Rwork0.23112 ---
obs0.26344 1264 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.831 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.15 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6190 0 0 406 6596
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 4842 -
Rwork0.24 87 -
obs--100 %

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