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- PDB-7zom: Crystal structure of N-terminal catalytic domain of human PLAAT3 -

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Basic information

Entry
Database: PDB / ID: 7zom
TitleCrystal structure of N-terminal catalytic domain of human PLAAT3
ComponentsPhospholipase A and acyltransferase 3
KeywordsHYDROLASE / NlpC/P60 / catalytic domain / phospholipase A and acyltransferase / enterovirus host factor / membrane remodelling
Function / homology
Function and homology information


membrane disassembly / regulation of adipose tissue development / ether lipid metabolic process / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS ...membrane disassembly / regulation of adipose tissue development / ether lipid metabolic process / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / phospholipase A1 activity / peroxisome organization / N-acyltransferase activity / phospholipase A2 activity / lens fiber cell differentiation / phospholipid biosynthetic process / phospholipase A2 / peroxisomal membrane / triglyceride metabolic process / acyltransferase activity / lipid catabolic process / phospholipid metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to bacterium / mitochondrial membrane / nuclear envelope / peroxisome / 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 / LRAT domain profile.
Similarity search - Domain/homology
Phospholipase A and acyltransferase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.601 Å
Authorsvon Castelmur, E. / Perrakis, A.
Funding support Switzerland, Netherlands, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: To Be Published
Title: Crystal structure of N-terminal catalytic domain of human PLAAT3
Authors: von Castelmur, E. / Perrakis, A.
History
DepositionApr 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A and acyltransferase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1804
Polymers14,8261
Non-polymers3553
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-27 kcal/mol
Surface area6450 Å2
Unit cell
Length a, b, c (Å)60.638, 60.638, 74.069
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Phospholipase A and acyltransferase 3 / Adipose-specific phospholipase A2 / AdPLA / Group XVI phospholipase A1/A2 / H-rev 107 protein ...Adipose-specific phospholipase A2 / AdPLA / Group XVI phospholipase A1/A2 / H-rev 107 protein homolog / H-REV107 / HREV107-1 / HRAS-like suppressor 1 / HRAS-like suppressor 3 / HRSL3 / HREV107-3 / Renal carcinoma antigen NY-REN-65


Mass: 14825.825 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAAT3, HRASLS3, HREV107, PLA2G16 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P53816, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, phospholipase A1, phospholipase A2
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes-NaOH pH7.0-7.5, 45-70% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97632 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97632 Å / Relative weight: 1
ReflectionResolution: 1.6→42.84 Å / Num. obs: 21212 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.021 / Rrim(I) all: 0.039 / Net I/σ(I): 21.4
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 999 / Rpim(I) all: 0.423 / Rrim(I) all: 0.779 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.601→42.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.076
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2091 1038 4.9 %
Rwork0.1846 20146 -
all0.186 --
obs-21184 99.671 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 38.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.056 Å20.528 Å20 Å2
2--1.056 Å2-0 Å2
3----3.426 Å2
Refinement stepCycle: LAST / Resolution: 1.601→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 24 51 928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012968
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.6571326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6755121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.11122.45353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65915175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.212156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02733
X-RAY DIFFRACTIONr_nbd_refined0.230.2353
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2635
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.251
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.214
X-RAY DIFFRACTIONr_mcbond_it5.4643.309438
X-RAY DIFFRACTIONr_mcangle_it6.2214.904549
X-RAY DIFFRACTIONr_scbond_it11.0474.042530
X-RAY DIFFRACTIONr_scangle_it11.6645.765767
X-RAY DIFFRACTIONr_lrange_it11.34745.3091371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.601-1.6420.281860.2791420X-RAY DIFFRACTION98.1747
1.642-1.6870.295920.2581419X-RAY DIFFRACTION99.8018
1.687-1.7360.264680.2421408X-RAY DIFFRACTION99.7972
1.736-1.7890.296780.2371335X-RAY DIFFRACTION100
1.789-1.8480.201640.2071318X-RAY DIFFRACTION99.9277
1.848-1.9130.234630.191263X-RAY DIFFRACTION99.6243
1.913-1.9850.232780.191229X-RAY DIFFRACTION99.8472
1.985-2.0660.223530.1921174X-RAY DIFFRACTION99.6751
2.066-2.1580.212500.1841160X-RAY DIFFRACTION99.7527
2.158-2.2630.204560.1761094X-RAY DIFFRACTION99.9131
2.263-2.3850.183470.1711056X-RAY DIFFRACTION99.9094
2.385-2.5290.229430.184992X-RAY DIFFRACTION99.8071
2.529-2.7030.192490.185908X-RAY DIFFRACTION99.7915
2.703-2.9190.187370.185899X-RAY DIFFRACTION99.7868
2.919-3.1970.212460.182801X-RAY DIFFRACTION100
3.197-3.5730.181340.174738X-RAY DIFFRACTION99.4845
3.573-4.1220.148340.149641X-RAY DIFFRACTION99.1189
4.122-5.0410.196290.147569X-RAY DIFFRACTION100
5.041-7.0960.223200.214444X-RAY DIFFRACTION100
7.096-42.840.34110.241278X-RAY DIFFRACTION98.9726

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