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- PDB-4fa0: Crystal structure of human AdPLA to 2.65 A resolution -

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Basic information

Entry
Database: PDB / ID: 4fa0
TitleCrystal structure of human AdPLA to 2.65 A resolution
ComponentsGroup XVI phospholipase A1/A2
KeywordsHYDROLASE / Phospholipase A2 / PLA2G16 / HRASLS3 / NlpC/P60 domain
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsLovell, S. / Battaile, K.P. / Addington, L. / Zhang, N. / Rao, J.L.U.M. / Moise, A.R.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure/Function relationships of adipose phospholipase A2 containing a cys-his-his catalytic triad.
Authors: Pang, X.Y. / Cao, J. / Addington, L. / Lovell, S. / Battaile, K.P. / Zhang, N. / Rao, J.L. / Dennis, E.A. / Moise, A.R.
History
DepositionMay 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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 / 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 A1/A2


Theoretical massNumber of molelcules
Total (without water)15,3101
Polymers15,3101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.991, 59.991, 74.006
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 Group XVI phospholipase A1/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: 15310.376 Da / Num. of mol.: 1 / Fragment: UNP residues 1-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G16, HRASLS3, HREV107 / Plasmid: pTBMalE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P53816, phospholipase A1, phospholipase A2

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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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 25% PEG 1500, 100mM MIB buffer, pH 5.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→51.954 Å / Num. all: 7196 / Num. obs: 7196 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.6
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.3 / Num. unique all: 796 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å42.56 Å
Translation2.5 Å42.56 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASER2.3.0phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
Aimlessdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2KYT

2kyt


Resolution: 2.65→30.14 Å / Cor.coef. Fo:Fc: 0.8576 / Cor.coef. Fo:Fc free: 0.8357 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.394 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ALTHOUGH THE DATA COULD BE PROCESSED TO 2.3A RESOLUTION, THERE WAS SEVERE ANISOTROPY IN THE A* AND B* DIRECTIONS AS DETERMINED FROM THE DIFFRACTION ANISOTROPY SERVER. THIS RESULTED IN VERY ...Details: ALTHOUGH THE DATA COULD BE PROCESSED TO 2.3A RESOLUTION, THERE WAS SEVERE ANISOTROPY IN THE A* AND B* DIRECTIONS AS DETERMINED FROM THE DIFFRACTION ANISOTROPY SERVER. THIS RESULTED IN VERY POOR CORRELATION BETWEEN FO AND FC AND HIGH PHASE ERRORS IN THE HIGHER RESOLUTION SHELLS USING DATA TO 2.3A RESOLUTION IN REFINEMENT. THEREFORE, THE MODEL WAS REFINED USING DATA TRUNCATED TO 2.65A RESOLUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 227 4.79 %RANDOM
Rwork0.2059 ---
obs0.2079 4743 99.94 %-
all-4743 --
Displacement parametersBiso max: 131.63 Å2 / Biso mean: 68.842 Å2 / Biso min: 42.36 Å2
Baniso -1Baniso -2Baniso -3
1--20.3886 Å20 Å20 Å2
2---20.3886 Å20 Å2
3---40.7772 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: LAST / Resolution: 2.65→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 0 0 802
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d359SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes20HARMONIC2
X-RAY DIFFRACTIONt_gen_planes119HARMONIC5
X-RAY DIFFRACTIONt_it825HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion103SEMIHARMONIC5
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_contact888SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d825HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1125HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion2.96
LS refinement shellResolution: 2.65→2.96 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2402 67 5.08 %
Rwork0.2407 1252 -
all0.2406 1319 -
obs-1319 99.94 %

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