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- PDB-4zxf: Crystal Structure of a Soluble Variant of Monoglyceride Lipase fr... -

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Basic information

Entry
Database: PDB / ID: 4zxf
TitleCrystal Structure of a Soluble Variant of Monoglyceride Lipase from Saccharomyces Cerevisiae in Complex with a Substrate Analog
ComponentsMonoglyceride lipase
KeywordsHYDROLASE / Monoglyceride Lipase / Monoacylglycerol Lipase / Complex / Substrate Analog
Function / homology
Function and homology information


acylglycerol lipase / triglyceride catabolic process / monoacylglycerol lipase activity / lipase activity / serine hydrolase activity / triglyceride metabolic process / lipid droplet / cell periphery / mitochondrial outer membrane / endoplasmic reticulum ...acylglycerol lipase / triglyceride catabolic process / monoacylglycerol lipase activity / lipase activity / serine hydrolase activity / triglyceride metabolic process / lipid droplet / cell periphery / mitochondrial outer membrane / endoplasmic reticulum / mitochondrion / membrane / plasma membrane / cytoplasm
Similarity search - Function
Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4S7 / NITRATE ION / Monoglyceride lipase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAschauer, P. / Lichtenegger, J. / Rengachari, S. / Gruber, K. / Oberer, M.
Funding support Austria, 2items
OrganizationGrant numberCountry
DK Molecular EnzymologyW901-B12 Austria
Austrian Science FundP24857 Austria
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Crystal structure of the Saccharomyces cerevisiae monoglyceride lipase Yju3p.
Authors: Aschauer, P. / Rengachari, S. / Lichtenegger, J. / Schittmayer, M. / Das, K.M. / Mayer, N. / Breinbauer, R. / Birner-Gruenberger, R. / Gruber, C.C. / Zimmermann, R. / Gruber, K. / Oberer, M.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Monoglyceride lipase
B: Monoglyceride lipase
C: Monoglyceride lipase
D: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,3559
Polymers155,6204
Non-polymers7355
Water2,720151
1
A: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0012
Polymers38,9051
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0012
Polymers38,9051
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3242
Polymers38,9051
Non-polymers4191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0293
Polymers38,9051
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.760, 107.130, 165.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Monoglyceride lipase / MGL / Monoacylglycerol hydrolase / MGH / Monoacylglycerol lipase / MAGL / Serine hydrolase YJU3


Mass: 38905.113 Da / Num. of mol.: 4 / Mutation: Q264R, L175S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YJU3, YKL094W, YKL441 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28321, acylglycerol lipase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-4S7 / 1-{3-[(R)-hydroxy(octadecyloxy)phosphoryl]propyl}triaza-1,2-dien-2-ium / octadecyl hydrogen (R)-(3-azidopropyl)phosphonate


Mass: 418.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H45N3O3P
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.43 Å3/Da / Density % sol: 49.31 % / Description: clustered plates
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 0.1 M Bicine/Trizma base pH 8.7, 10% w/v PEG 20 000, 20% v/v PEG MME 550 and 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulphate, Microseeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97939 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.5→165.45 Å / Num. all: 47793 / Num. obs: 47793 / % possible obs: 99.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 43.76 Å2 / Rpim(I) all: 0.093 / Rrim(I) all: 0.202 / Rsym value: 0.179 / Net I/av σ(I): 3.6 / Net I/σ(I): 6.5 / Num. measured all: 215498
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.644.20.8460.82911068690.4550.8461.899.6
2.64-2.84.80.70713119565060.3570.7072.399.9
2.8-2.994.60.5481.32849361770.2830.5482.999.8
2.99-3.234.20.3741.92417056920.20.374499.4
3.23-3.544.80.2482.92523652990.1260.2486.299.8
3.54-3.954.60.1564.52230348120.080.1569.199.8
3.95-4.564.40.09871882742820.0520.09812.399.7
4.56-5.594.70.0857.91690736240.0430.08513.499.7
5.59-7.914.30.0768.91229128610.040.07612.199.3
7.91-82.7254.20.04613696616710.0240.04618.399.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZWN

4zwn


Resolution: 2.5→65.476 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 2409 5.05 %
Rwork0.2013 --
obs0.2041 47713 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→65.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9756 0 45 151 9952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410072
X-RAY DIFFRACTIONf_angle_d0.80613579
X-RAY DIFFRACTIONf_dihedral_angle_d14.0743754
X-RAY DIFFRACTIONf_chiral_restr0.041389
X-RAY DIFFRACTIONf_plane_restr0.0041762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55110.37621170.31372640X-RAY DIFFRACTION99
2.5511-2.60650.37651270.30162610X-RAY DIFFRACTION99
2.6065-2.66720.35181590.2932613X-RAY DIFFRACTION100
2.6672-2.73390.3531440.27782648X-RAY DIFFRACTION100
2.7339-2.80780.3041540.25472625X-RAY DIFFRACTION100
2.8078-2.89040.32841410.25242628X-RAY DIFFRACTION100
2.8904-2.98370.27441630.24382633X-RAY DIFFRACTION100
2.9837-3.09030.35431610.23942615X-RAY DIFFRACTION99
3.0903-3.21410.29231350.22442630X-RAY DIFFRACTION99
3.2141-3.36030.2761470.21122643X-RAY DIFFRACTION100
3.3603-3.53750.25281440.20082647X-RAY DIFFRACTION100
3.5375-3.75910.23171370.18932683X-RAY DIFFRACTION100
3.7591-4.04930.21571250.17652712X-RAY DIFFRACTION100
4.0493-4.45670.20421280.15612701X-RAY DIFFRACTION100
4.4567-5.10140.21821450.1582704X-RAY DIFFRACTION100
5.1014-6.42640.23011430.17812711X-RAY DIFFRACTION99
6.4264-65.49840.20791390.17662861X-RAY DIFFRACTION99

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