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- PDB-4ke8: Crystal structure of Monoglyceride lipase from Bacillus sp. H257 ... -

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Basic information

Entry
Database: PDB / ID: 4ke8
TitleCrystal structure of Monoglyceride lipase from Bacillus sp. H257 in complex with monopalmitoyl glycerol analogue
ComponentsThermostable monoacylglycerol lipase
KeywordsHYDROLASE / alpha/beta hydrolase / monoglyceride lipase
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
Chem-1QY / Thermostable monoacylglycerol lipase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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: Refinement description / Category: software
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6888
Polymers118,2424
Non-polymers1,4464
Water16,250902
1
A: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9222
Polymers29,5611
Non-polymers3611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9222
Polymers29,5611
Non-polymers3611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9222
Polymers29,5611
Non-polymers3611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9222
Polymers29,5611
Non-polymers3611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.015, 81.125, 85.611
Angle α, β, γ (deg.)90.00, 100.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thermostable monoacylglycerol lipase / MGLP


Mass: 29560.611 Da / Num. of mol.: 4
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-1QY / tetradecyl hydrogen (R)-(3-azidopropyl)phosphonate


Mass: 361.460 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H36N3O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 902 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.2
Details: 0.1 M citric acid pH 5.2 and 18% PEG 3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→43.737 Å / Num. all: 88070 / Num. obs: 88070 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rsym value: 0.041 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.85-1.953.30.3022.50.302199.6
1.95-2.073.20.174.40.17199.8
2.07-2.213.50.1246.10.124199.9
2.21-2.393.50.09380.093199.5
2.39-2.623.40.061120.061199.8
2.62-2.933.20.04316.70.043199.7
2.93-3.383.50.02922.20.029199.4
3.38-4.143.40.02326.90.023198.7
4.14-5.853.10.01831.70.018199
5.85-43.7373.50.01528.60.015198.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
BALBESphasing
SCALA3.3.16data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→43.737 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.18 / σ(F): 1.5 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 1999 2.45 %
Rwork0.1799 --
obs0.1809 81489 92.03 %
all-81492 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.4392 Å20 Å20.4305 Å2
2--17.2794 Å2-0 Å2
3----7.8403 Å2
Refinement stepCycle: LAST / Resolution: 1.85→43.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7651 0 92 902 8645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077951
X-RAY DIFFRACTIONf_angle_d1.04310811
X-RAY DIFFRACTIONf_dihedral_angle_d13.4022855
X-RAY DIFFRACTIONf_chiral_restr0.0651202
X-RAY DIFFRACTIONf_plane_restr0.0051391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89630.30561200.24384769X-RAY DIFFRACTION77
1.8963-1.94750.27241280.27045092X-RAY DIFFRACTION83
1.9475-2.00480.29751330.22595269X-RAY DIFFRACTION86
2.0048-2.06960.25561390.20955532X-RAY DIFFRACTION90
2.0696-2.14350.2351430.20395715X-RAY DIFFRACTION93
2.1435-2.22930.26561360.19245363X-RAY DIFFRACTION87
2.2293-2.33080.27381380.20345517X-RAY DIFFRACTION90
2.3308-2.45370.1971500.18265909X-RAY DIFFRACTION96
2.4537-2.60740.22841480.18335924X-RAY DIFFRACTION96
2.6074-2.80870.23841510.18726014X-RAY DIFFRACTION98
2.8087-3.09120.23141530.1936042X-RAY DIFFRACTION98
3.0912-3.53840.23591520.17926104X-RAY DIFFRACTION98
3.5384-4.45730.17731530.14886061X-RAY DIFFRACTION98
4.4573-43.74880.16041550.13976179X-RAY DIFFRACTION98

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