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- PDB-4pka: Crystal structure of patatin aged with diisopropylphosphorofluoridate -

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Basic information

Entry
Database: PDB / ID: 4pka
TitleCrystal structure of patatin aged with diisopropylphosphorofluoridate
ComponentsPatatin-17
KeywordsHYDROLASE / alpha/beta class fold with approximately three layers / serine hydrolase
Function / homology
Function and homology information


phospholipase activity / acylglycerol 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWijeyesakere, S.J. / Richardson, R.J. / Stuckey, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
Army Research OfficeDAAD19-02-1-0388 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES07062 United States
University of Michigan Rackham School of Graduate Studies United States
CitationJournal: Plos One / Year: 2014
Title: Crystal Structure of Patatin-17 in Complex with Aged and Non-Aged Organophosphorus Compounds.
Authors: Wijeyesakere, S.J. / Richardson, R.J. / Stuckey, J.A.
History
DepositionMay 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
X: Patatin-17


Theoretical massNumber of molelcules
Total (without water)41,3871
Polymers41,3871
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Patatin-17

X: Patatin-17


Theoretical massNumber of molelcules
Total (without water)82,7732
Polymers82,7732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area5890 Å2
ΔGint-55 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.990, 52.990, 242.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Patatin-17


Mass: 41386.535 Da / Num. of mol.: 1 / Fragment: UNP residues 23-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum cardiophyllum (heartleaf nightshade)
Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): CD41
References: UniProt: Q8LPW4, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, 46% v/v PEG400, 75 mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97626 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2007 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.6→44.332 Å / Num. all: 10963 / Num. obs: 10963 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 58.06 Å2 / Rsym value: 0.072 / Net I/σ(I): 20
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3 / Num. unique all: 995 / Rsym value: 0.483 / % possible all: 87.8

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.8.0refinement
Omodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.332 Å / Cor.coef. Fo:Fc: 0.9259 / Cor.coef. Fo:Fc free: 0.8819 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2781 529 4.83 %RANDOM
Rwork0.2099 ---
obs0.2131 10963 95.3 %-
all-10963 --
Displacement parametersBiso mean: 45.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.4786 Å20 Å20 Å2
2--1.4786 Å20 Å2
3----2.9573 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: LAST / Resolution: 2.6→44.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 0 37 2809
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092827HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.063842HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1308SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes403HARMONIC5
X-RAY DIFFRACTIONt_it2827HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion3
X-RAY DIFFRACTIONt_chiral_improper_torsion384SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3509SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.85 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3478 137 5.79 %
Rwork0.2396 2229 -
all0.2459 2366 -

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