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- PDB-6qe2: Crystal structure of Paleococcus ferrophilus monoacylglycerol lipase. -

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Basic information

Entry
Database: PDB / ID: 6qe2
TitleCrystal structure of Paleococcus ferrophilus monoacylglycerol lipase.
ComponentsMonoacylglycerol lipase
KeywordsHYDROLASE / Monoacylglycerol lipase / Monoglyceride lipase / MAGL / MGL
Biological speciesPalaeococcus ferrophilus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7461 Å
AuthorsLabar, G. / Demarez, M. / Brandt, N. / Wouters, J. / Leherte, F.
Funding support Belgium, 2items
OrganizationGrant numberCountry
BAG-Belgium 20151139 Belgium
BAG-Belgium 20161175 Belgium
CitationJournal: Biomolecules / Year: 2021
Title: Structure and Dynamics of an Archeal Monoglyceride Lipase from Palaeococcus ferrophilus as Revealed by Crystallography and In Silico Analysis.
Authors: Labar, G. / Brandt, N. / Flaba, A. / Wouters, J. / Leherte, L.
History
DepositionJan 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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

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Assembly

Deposited unit
A: Monoacylglycerol lipase
B: Monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5356
Polymers62,8922
Non-polymers6434
Water10,467581
1
A: Monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7683
Polymers31,4461
Non-polymers3212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7683
Polymers31,4461
Non-polymers3212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.600, 75.460, 85.440
Angle α, β, γ (deg.)90.000, 128.290, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Monoacylglycerol lipase


Mass: 31446.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: hexa-histidine tag / Source: (gene. exp.) Palaeococcus ferrophilus (archaea) / Plasmid: pET30b / Production host: Escherichia coli BL21 (bacteria) / References: acylglycerol lipase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 49.3 %
Crystal growTemperature: 293.15 K / Method: microbatch
Details: Protein solution ( 15 mg/mL in Hepes 20 mM pH 8.1, NaCl 150 mM, LDAO 0.1 %, Glycerol 10% m/m) mixed with an equal volume of PEG 3350 20 %, potassium formate 0.2 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 11, 2016
RadiationMonochromator: Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.7461→35.664 Å / Num. obs: 60488 / % possible obs: 98.6 % / Redundancy: 3.651 % / Biso Wilson estimate: 27.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.053 / Χ2: 1.138 / Net I/σ(I): 13.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.793.5260.3822.3341040.9360.44890.7
1.79-1.843.8190.3043.1444120.960.35399.7
1.84-1.893.8120.2453.9742240.9740.28599.7
1.89-1.953.8080.1945.0441480.9810.22599.6
1.95-2.023.7930.1546.4939900.9870.17999.7
2.02-2.093.7660.1248.2539190.9910.14599.6
2.09-2.173.7560.1089.7737330.9920.12599.4
2.17-2.253.7120.0911.835980.9930.10599.3
2.25-2.353.6650.07713.7934580.9950.0999.5
2.35-2.473.5960.0715.3733020.9950.08299.2
2.47-2.63.4940.06516.9331290.9940.07799.1
2.6-2.763.3260.05818.3229630.9950.06998.2
2.76-2.952.9470.04919.6927630.9960.0698.3
2.95-3.193.3380.04523.4826060.9960.05498.8
3.19-3.493.7120.0427.9223930.9970.04699.2
3.49-3.93.7330.03829.8221840.9980.04499.1
3.9-4.513.8050.03531.1819400.9980.0499.1
4.51-5.523.8480.03231.7416420.9980.03799.2
5.52-7.813.8520.03131.812740.9980.03599
7.81-35.6643.6220.02832.057060.9980.03395.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.11_2563refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hju

3hju


Resolution: 1.7461→35.664 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.53
RfactorNum. reflection% reflection
Rfree0.1975 3025 5.01 %
Rwork0.1712 --
obs0.1725 60415 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.74 Å2 / Biso mean: 34.1502 Å2 / Biso min: 16.29 Å2
Refinement stepCycle: final / Resolution: 1.7461→35.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 44 581 4643
Biso mean--44.21 45.85 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074218
X-RAY DIFFRACTIONf_angle_d0.9145696
X-RAY DIFFRACTIONf_chiral_restr0.061608
X-RAY DIFFRACTIONf_plane_restr0.006728
X-RAY DIFFRACTIONf_dihedral_angle_d17.2531617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7461-1.77330.39371190.3082235235485
1.7733-1.80240.27641390.247926192758100
1.8024-1.83350.30151380.233726212759100
1.8335-1.86680.24461390.215126222761100
1.8668-1.90270.26271370.21326112748100
1.9027-1.94160.24851380.212426032741100
1.9416-1.98380.25191390.212626512790100
1.9838-2.02990.26171370.19226202757100
2.0299-2.08070.23871380.189826062744100
2.0807-2.13690.2411380.187526142752100
2.1369-2.19980.21441370.177626222759100
2.1998-2.27080.21251380.184426202758100
2.2708-2.3520.17841380.178726242762100
2.352-2.44610.23061400.182626462786100
2.4461-2.55740.23141360.173525912727100
2.5574-2.69220.2161380.18192596273499
2.6922-2.86080.21011370.17732633277099
2.8608-3.08160.20331380.17722608274699
3.0816-3.39150.19361390.168626462785100
3.3915-3.88170.16381390.153426392778100
3.8817-4.88850.15851400.139226552795100
4.8885-35.67130.1631430.15762708285199

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