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- PDB-4ke6: Crystal structure D196N mutant of Monoglyceride lipase from Bacil... -

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Basic information

Entry
Database: PDB / ID: 4ke6
TitleCrystal structure D196N mutant of Monoglyceride lipase from Bacillus sp. H257 in complex with 1-rac-lauroyl glycerol
ComponentsThermostable monoacylglycerol lipase
KeywordsHYDROLASE / alpha/beta hydrolase fold / Monoglyceride Lipase / Monoglycerides
Function / homology
Function and homology information


acylglycerol lipase / monoacylglycerol lipase activity
Similarity search - Function
Esterase/lipase / : / 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
(2R)-2,3-dihydroxypropyl dodecanoate / Thermostable monoacylglycerol lipase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsRengachari, S. / Aschauer, P. / Gruber, K. / Dreveny, I. / Oberer, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Conformational plasticity and ligand binding of bacterial monoacylglycerol lipase.
Authors: Rengachari, S. / Aschauer, P. / Schittmayer, M. / Mayer, N. / Gruber, K. / Breinbauer, R. / Birner-Gruenberger, R. / Dreveny, I. / Oberer, M.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermostable monoacylglycerol lipase
B: Thermostable monoacylglycerol lipase
C: Thermostable monoacylglycerol lipase
D: Thermostable monoacylglycerol lipase
E: Thermostable monoacylglycerol lipase
F: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,10511
Polymers177,3586
Non-polymers7475
Water55831
1
A: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8342
Polymers29,5601
Non-polymers2741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thermostable monoacylglycerol lipase


Theoretical massNumber of molelcules
Total (without water)29,5601
Polymers29,5601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6782
Polymers29,5601
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thermostable monoacylglycerol lipase


Theoretical massNumber of molelcules
Total (without water)29,5601
Polymers29,5601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6782
Polymers29,5601
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7963
Polymers29,5601
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.185, 182.878, 248.264
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
Thermostable monoacylglycerol lipase / MGLP


Mass: 29559.623 Da / Num. of mol.: 6 / Mutation: D196N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: H-257 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P82597, acylglycerol lipase
#2: Chemical ChemComp-1QW / (2R)-2,3-dihydroxypropyl dodecanoate / 1-Lauroyl-rac-glycerol


Mass: 274.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30O4
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: ~0.9 mM of bMGL(D196N) was mixed with 180 mM 1-(rac)-lauroyl glycerol dissolved in 99% EtOH to achieve a final protein-ligand ratio of 1:5. The protein-ligand mixture was incubated at 4 C ...Details: ~0.9 mM of bMGL(D196N) was mixed with 180 mM 1-(rac)-lauroyl glycerol dissolved in 99% EtOH to achieve a final protein-ligand ratio of 1:5. The protein-ligand mixture was incubated at 4 C for 1 hour. Initial crystals were obtained using the Morpheus screen in condition A4. These crystals were used for preparing a seed stock. The optimised crystals were obtained in a drop containing 0.9 mM bMGL(D196N); 56 % v/v MPD, 0.1 M HEPES pH 6.9 and 1:1000 dilution of seed stock in a ratio of 2:2:1 respectively. 1-LG powder was added to these crystallization drops and the crystals were soaked for 8h., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 22, 2013 / Details: mirrors
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→73.621 Å / Num. all: 42482 / Num. obs: 42482 / % possible obs: 94.4 % / Redundancy: 3.9 % / Rsym value: 0.096 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.8-2.953.10.4011.90.401187.6
2.95-3.133.80.3032.50.303192.1
3.13-3.354.10.2133.50.213197.8
3.35-3.6140.1611.80.161197.5
3.61-3.9640.1114.70.111197.2
3.96-4.434.10.0749.50.074196.7
4.43-5.114.20.05811.50.058195.8
5.11-6.264.20.079.50.07195.2
6.26-8.854.20.04613.70.046192.7
8.85-73.62140.03415.80.034189.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.4 Å73.62 Å
Translation3.4 Å73.62 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASER2.5.2phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→61.357 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.37 / σ(F): 1.35 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 2152 5.08 %
Rwork0.1998 --
obs0.2021 42399 93.31 %
all-42401 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.0619 Å2
Refinement stepCycle: LAST / Resolution: 2.8→61.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11022 0 51 31 11104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811367
X-RAY DIFFRACTIONf_angle_d1.3615472
X-RAY DIFFRACTIONf_dihedral_angle_d13.9334144
X-RAY DIFFRACTIONf_chiral_restr0.0661741
X-RAY DIFFRACTIONf_plane_restr0.0091991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.86520.36831450.2782403X-RAY DIFFRACTION88
2.8652-2.93690.36081440.27792422X-RAY DIFFRACTION87
2.9369-3.01630.34071150.26372460X-RAY DIFFRACTION84
3.0163-3.1050.32741720.25662640X-RAY DIFFRACTION96
3.105-3.20520.30861550.23932770X-RAY DIFFRACTION98
3.2052-3.31980.28521380.22312753X-RAY DIFFRACTION97
3.3198-3.45270.25551350.21022740X-RAY DIFFRACTION97
3.4527-3.60980.24361550.20412779X-RAY DIFFRACTION97
3.6098-3.80010.26491340.20462749X-RAY DIFFRACTION97
3.8001-4.03810.23651530.18772753X-RAY DIFFRACTION96
4.0381-4.34990.21171280.17262821X-RAY DIFFRACTION95
4.3499-4.78740.20291550.16222727X-RAY DIFFRACTION96
4.7874-5.47980.19481540.17582733X-RAY DIFFRACTION94
5.4798-6.90250.24881290.20452733X-RAY DIFFRACTION92
6.9025-61.37220.19691400.17852764X-RAY DIFFRACTION87

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