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- PDB-1oxw: The Crystal Structure of SeMet Patatin -

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Basic information

Entry
Database: PDB / ID: 1oxw
TitleThe Crystal Structure of SeMet Patatin
ComponentsPatatin
KeywordsPLANT PROTEIN / ALPHA/BETA CLASS FOLD WITH APPROXIMATELY THREE LAYERS / ALPHA/BETA/ALPHA IN CONTENT. POSSESSES A CENTRAL SIX-STRANDED BETA SHEET WITH ALPHA-HELICES FRONT & BACK
Function / homology
Function and homology information


phospholipase activity / monoacylglycerol lipase activity / nutrient reservoir activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / vacuole / lipid catabolic process / defense response
Similarity search - Function
Cytosolic phospholipase A2 catalytic domain / Cytosolic phospholipase A2 catalytic domain / Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / Acyl transferase/acyl hydrolase/lysophospholipase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSolanum cardiophyllum (heartleaf nightshade)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsRydel, T.J. / Williams, J.M. / Krieger, E. / Moshiri, F. / Stallings, W.C. / Brown, S.M. / Pershing, J.C. / Purcell, J.P. / Alibhai, M.F.
CitationJournal: Biochemistry / Year: 2003
Title: The Crystal Structure, Mutagenesis, and Activity Studies Reveal that Patatin Is a Lipid Acyl Hydrolase with a Ser-Asp Catalytic Dyad
Authors: Rydel, T.J. / Williams, J.M. / Krieger, E. / Moshiri, F. / Stallings, W.C. / Brown, S.M. / Pershing, J.C. / Purcell, J.P. / Alibhai, M.F.
History
DepositionApr 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Patatin
B: Patatin
C: Patatin


Theoretical massNumber of molelcules
Total (without water)125,6223
Polymers125,6223
Non-polymers00
Water8,971498
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.180, 171.420, 129.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein Patatin


Mass: 41874.105 Da / Num. of mol.: 3 / Mutation: SeMet enzyme; N-term. hexa-His tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum cardiophyllum (heartleaf nightshade)
Plasmid: pET / Production host: Escherichia coli (E. coli) / Variant (production host): B834(DE3) / References: UniProt: Q8LPW4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 3350, AMMONIUM ACETATE, TRIS BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMTris1droppH7.4
316 %PEG33501reservoir
40.24 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9791, 0.9792, 1.019, 0.9419
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 25, 1999
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97921
31.0191
40.94191
ReflectionResolution: 2.2→20 Å / Num. all: 55374 / Num. obs: 51877 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 14.3 % / Rsym value: 0.086 / Net I/σ(I): 36.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.95 % / Mean I/σ(I) obs: 7 / Num. unique all: 5450 / Rsym value: 0.273 / % possible all: 80.4
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 55261 / % possible obs: 100 % / Redundancy: 13.8 % / Num. measured all: 762165 / Rmerge(I) obs: 0.077

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
SOLVE& AMoREphasing
X-PLOR98.1refinement
AMoREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Isotropic thermal model: Isotropic / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 5221 -RANDOM
Rwork0.22 ---
all-55374 --
obs-51876 100 %-
Displacement parametersBiso mean: 30.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8373 0 0 498 8871
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.272
LS refinement shellResolution: 2.2→2.3 Å
RfactorNum. reflection% reflection
Rfree0.3396 580 -
Rwork0.2733 --
obs-5747 100 %
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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