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- PDB-3rli: Crystal structure of monoacylglycerol lipase from Bacillus sp. H2... -

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Basic information

Entry
Database: PDB / ID: 3rli
TitleCrystal structure of monoacylglycerol lipase from Bacillus sp. H257 in complex with PMSF
ComponentsThermostable monoacylglycerol lipase
KeywordsHYDROLASE / alpha/beta hydrolase
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
phenylmethanesulfonic acid / Thermostable monoacylglycerol lipase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.854 Å
AuthorsRengachari, S. / Bezerra, G.A. / Gruber, K. / Oberer, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: The structure of monoacylglycerol lipase from Bacillus sp. H257 reveals unexpected conservation of the cap architecture between bacterial and human enzymes.
Authors: Rengachari, S. / Bezerra, G.A. / Riegler-Berket, L. / Gruber, C.C. / Sturm, C. / Taschler, U. / Boeszoermenyi, A. / Dreveny, I. / Zimmermann, R. / Gruber, K. / Oberer, M.
History
DepositionApr 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8513
Polymers29,5611
Non-polymers2902
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.050, 70.690, 43.440
Angle α, β, γ (deg.)90.000, 111.650, 90.000
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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: H257 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P82597, acylglycerol lipase
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.84 Å3/Da / Density % sol: 33.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, and 0.02 M of monosaccharides (D-glucose, D-mannose, D-galactose, L-fuctose, D-xylose, and N-acetyl-D- ...Details: 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, and 0.02 M of monosaccharides (D-glucose, D-mannose, D-galactose, L-fuctose, D-xylose, and N-acetyl-D-glucosamine), VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2010
RadiationMonochromator: Si 111, horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.854→40.376 Å / Num. all: 17878 / Num. obs: 17878 / % possible obs: 96.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.56 Å2 / Rsym value: 0.057
Reflection shellResolution: 1.854→1.94 Å / % possible all: 96.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 27.63
Highest resolutionLowest resolution
Rotation2.5 Å26.59 Å
Translation2.5 Å26.59 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RM3

3rm3


Resolution: 1.854→17.683 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.8828 / SU ML: 0.21 / σ(F): 0 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1939 889 5.06 %
Rwork0.156 --
obs0.1579 17561 96.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.738 Å2 / ksol: 0.437 e/Å3
Displacement parametersBiso max: 71.65 Å2 / Biso mean: 17.4197 Å2 / Biso min: 4.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.6174 Å20 Å2-0.3725 Å2
2--0.1538 Å20 Å2
3----0.7713 Å2
Refinement stepCycle: LAST / Resolution: 1.854→17.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 18 202 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131971
X-RAY DIFFRACTIONf_angle_d1.0512685
X-RAY DIFFRACTIONf_chiral_restr0.066300
X-RAY DIFFRACTIONf_plane_restr0.005347
X-RAY DIFFRACTIONf_dihedral_angle_d14.173720
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.854-1.97050.27211420.2142617275991
1.9705-2.12240.23171630.172778294197
2.1224-2.33560.21911460.15982799294598
2.3356-2.67260.21621420.15892837297998
2.6726-3.36330.17491640.14862821298598
3.3633-17.68370.15111320.13972820295296

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