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- PDB-4dot: Crystal structure of human HRASLS3. -

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Basic information

Entry
Database: PDB / ID: 4dot
TitleCrystal structure of human HRASLS3.
ComponentsGroup XVI phospholipase A2
KeywordsHYDROLASE / alpha/beta fold / phospholipase/acyltransferase / phosphatidylcholine / phosphatidylethanolamine / membrane
Function / homology
Function and homology information


membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity ...membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / peroxisome organization / N-acyltransferase activity / phospholipid biosynthetic process / phospholipase A2 activity / lens fiber cell differentiation / phospholipase A2 / peroxisomal membrane / triglyceride metabolic process / acyltransferase activity / localization / phospholipid metabolic process / lipid catabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mitochondrial membrane / response to bacterium / peroxisome / nuclear envelope / lysosome / lysosomal membrane / lipid binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Lecithin retinol acyltransferase / LRAT domain profile. / LRAT domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Phospholipase A and acyltransferase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.96 Å
AuthorsKiser, P.D. / Golczak, M. / Sears, A.E. / Lodowski, D.T. / Palczewski, K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Basis for the Acyltransferase Activity of Lecithin:Retinol Acyltransferase-like Proteins.
Authors: Golczak, M. / Kiser, P.D. / Sears, A.E. / Lodowski, D.T. / Blaner, W.S. / Palczewski, K.
History
DepositionFeb 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Group XVI phospholipase A2


Theoretical massNumber of molelcules
Total (without water)15,8971
Polymers15,8971
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.446, 62.446, 73.922
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Group XVI phospholipase A2 / Adipose-specific phospholipase A2 / AdPLA / H-rev 107 protein homolog / HRAS-like suppressor 1 / ...Adipose-specific phospholipase A2 / AdPLA / H-rev 107 protein homolog / HRAS-like suppressor 1 / HRAS-like suppressor 3 / HRSL3 / HREV107-1 / HREV107-3 / Renal carcinoma antigen NY-REN-65


Mass: 15896.979 Da / Num. of mol.: 1 / Fragment: HRASLS3 N-terminus, UNP residues 1-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G16, HRASLS3, HREV107 / Production host: Escherichia coli (E. coli)
References: UniProt: P53816, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-TRIS, 28% PEG MME 2000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 8365 / Num. obs: 8365 / % possible obs: 68.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.95→2.07 Å / % possible all: 5.3

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
REFMAC5.6.0117refinement
XDSdata reduction
RefinementMethod to determine structure: MIR / Resolution: 1.96→30.51 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.358 / SU ML: 0.125 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21634 393 4.7 %RANDOM
Rwork0.20322 ---
obs0.20386 7900 67.36 %-
all-7900 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.96→30.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 0 43 873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02866
X-RAY DIFFRACTIONr_bond_other_d0.0010.02604
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9671177
X-RAY DIFFRACTIONr_angle_other_deg0.96331471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1665104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.85323.95343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95415145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.893155
X-RAY DIFFRACTIONr_chiral_restr0.080.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021953
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02176
LS refinement shellResolution: 1.965→2.015 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 2 -
Rwork0.395 29 -
obs--3.42 %
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)
14.77561.22030.93152.27762.645313.97120.11250.1165-0.08160.1644-0.14010.1528-0.0158-0.81890.02760.1477-0.00640.02050.0569-0.02260.15361.915135.89722.1063
213.2058-1.8714-2.84453.59181.28939.99210.06070.34631.341-0.37250.001-0.1626-1.4808-0.1976-0.06170.5326-0.0608-0.02530.0330.02460.317710.707245.09251.4776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 78
2X-RAY DIFFRACTION2A79 - 125

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