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- PDB-4pk9: The Crystal Structure of Native Patatin -

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Basic information

Entry
Database: PDB / ID: 4pk9
TitleThe Crystal Structure of Native Patatin
ComponentsPatatin-17
KeywordsHYDROLASE / alpha/beta class fold with approximately three layers / serine hydrolase
Function / homology
Function and homology information


nutrient reservoir activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / vacuole / lipid catabolic process / defense response / hydrolase activity
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: 1.96 Å
AuthorsWijeyesakere, S.J. / Stuckey, J.A. / Richardson, R.J.
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
Michigan Economic Development Corporation085P1000817 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 1.1Oct 8, 2014Group: Database references
Revision 1.2Sep 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 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Patatin-17


Theoretical massNumber of molelcules
Total (without water)41,2641
Polymers41,2641
Non-polymers00
Water2,288127
1


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

A: Patatin-17


Theoretical massNumber of molelcules
Total (without water)82,5292
Polymers82,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area5660 Å2
ΔGint-57 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.316, 53.316, 244.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-444-

HOH

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Components

#1: Protein Patatin-17 /


Mass: 41264.480 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 / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, 49% v/v PEG400, 225 mM cesium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2008 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.96→48.885 Å / Num. all: 26718 / Num. obs: 24922 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 26.55 Å2 / Rsym value: 0.076 / Net I/σ(I): 20
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 5 / Rsym value: 0.274 / % possible all: 76.4

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OXW

1oxw


Resolution: 1.96→22.32 Å / Cor.coef. Fo:Fc: 0.9285 / Cor.coef. Fo:Fc free: 0.9147 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood refinement in AUTOBUSTER
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 1263 5.09 %RANDOM
Rwork0.1928 ---
obs0.1943 24814 93.2 %-
all-24814 --
Displacement parametersBiso mean: 28.92 Å2
Baniso -1Baniso -2Baniso -3
1-2.3709 Å20 Å20 Å2
2--2.3709 Å20 Å2
3----4.7418 Å2
Refine analyzeLuzzati coordinate error obs: 0.206 Å
Refinement stepCycle: LAST / Resolution: 1.96→22.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 0 127 2909
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012882HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.993921HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1341SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes80HARMONIC2
X-RAY DIFFRACTIONt_gen_planes415HARMONIC5
X-RAY DIFFRACTIONt_it2882HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 1.96→2.05 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2168 122 4.86 %
Rwork0.1838 2390 -
all0.1855 2512 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4109-0.0753-0.25860.79010.04630.25770.02810.04960.031-0.0759-0.0383-0.06940.0160.03460.0102-0.02140.00760.0187-0.01250.0028-0.0243-17.331722.9761-21.601
20.0002-0.16840.03351.81050.02640-0.0029-0.0542-0.02550.0198-0.01120.08660.00470.00620.0141-0.0184-0.00540.0146-0.0176-0.0030.01-30.278833.4338-16.8004
30.18850.02460.08410.41590.12430.5131-0.01760.01540.0434-0.004-0.00210.0678-0.0384-0.02440.0196-0.03270.01160.0236-0.0227-0.0105-0.0103-22.933129.8881-8.4054
41.0470.97570.30981.1705-0.08480.8135-0.0058-0.067-0.04080.1109-0.091-0.0556-0.06560.05120.0968-0.00920.0088-0.0002-0.0158-0.0036-0.0146-18.171519.5261-1.7776
51.24191.55520.16492.34770.08850.53880.0018-0.0121-0.02150.0753-0.0385-0.13180.11950.03040.0366-0.03240.03570.049-0.0509-0.0131-0.0171-14.94929.618-12.6818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|24 - A|146 }A24 - 146
2X-RAY DIFFRACTION2{ A|147 - A|181 }A147 - 181
3X-RAY DIFFRACTION3{ A|182 - A|285 }A182 - 285
4X-RAY DIFFRACTION4{ A|286 - A|331 }A286 - 331
5X-RAY DIFFRACTION5{ A|332 - A|382 }A332 - 382

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