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- PDB-3rm3: Crystal structure of monoacylglycerol lipase from Bacillus sp. H257 -

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Basic information

Entry
Database: PDB / ID: 3rm3
TitleCrystal structure of monoacylglycerol lipase from Bacillus sp. H257
ComponentsThermostable monoacylglycerol lipase
KeywordsHYDROLASE / alpha/beta hydrolase fold
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
Thermostable monoacylglycerol lipase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 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 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 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 / pdbx_initial_refinement_model / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6792
Polymers29,5611
Non-polymers1181
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.150, 71.210, 43.660
Angle α, β, γ (deg.)90.00, 111.70, 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.: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1.87 Å3/Da / Density % sol: 34.14 %
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 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2010
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 5.2 / Number: 249649 / Rsym value: 0.065 / D res high: 1.2 Å / D res low: 40.566 Å / Num. obs: 67545 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
3.7917.7296.610.0480.0483.6
2.683.7910010.0490.0493.8
2.192.6810010.0590.0593.8
1.92.1910010.0640.0643.8
1.71.910010.0710.0713.8
1.551.710010.0910.0913.7
1.431.5510010.1310.1313.7
1.341.4310010.1910.1913.7
1.261.3499.910.2520.2523.6
1.21.2699.810.3460.3463.6
ReflectionResolution: 1.2→40.566 Å / Num. all: 67545 / Num. obs: 67545 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rsym value: 0.065 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.2-1.263.60.3462.20.346199.8
1.26-1.343.60.25230.252199.9
1.34-1.433.70.1913.90.1911100
1.43-1.553.70.1315.50.1311100
1.55-1.73.70.0917.40.0911100
1.7-1.93.80.07190.0711100
1.9-2.193.80.0649.10.0641100
2.19-2.683.80.0599.90.0591100
2.68-3.793.80.04910.60.0491100
3.79-17.7233.60.04811.40.048196.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R1D

1r1d


Resolution: 1.2→17.723 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.13 / σ(F): 1.36 / Phase error: 11.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1579 3417 5.06 %
Rwork0.1346 --
obs0.1358 67516 99.84 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.847 Å2 / ksol: 0.446 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0477 Å20 Å20.0226 Å2
2--0.0221 Å2-0 Å2
3----0.0697 Å2
Refinement stepCycle: LAST / Resolution: 1.2→17.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 8 234 2142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071997
X-RAY DIFFRACTIONf_angle_d1.1912727
X-RAY DIFFRACTIONf_dihedral_angle_d11.81735
X-RAY DIFFRACTIONf_chiral_restr0.075307
X-RAY DIFFRACTIONf_plane_restr0.007353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21710.23451550.21522653X-RAY DIFFRACTION100
1.2171-1.23530.20421280.19262649X-RAY DIFFRACTION99
1.2353-1.25460.20641240.17922687X-RAY DIFFRACTION100
1.2546-1.27520.18891470.1562658X-RAY DIFFRACTION99
1.2752-1.29710.17131600.15162627X-RAY DIFFRACTION100
1.2971-1.32070.18341310.13742713X-RAY DIFFRACTION100
1.3207-1.34610.16681290.12282665X-RAY DIFFRACTION100
1.3461-1.37360.15471570.12182646X-RAY DIFFRACTION100
1.3736-1.40340.20451460.11622665X-RAY DIFFRACTION100
1.4034-1.43610.13961460.10872642X-RAY DIFFRACTION100
1.4361-1.4720.1171310.10152694X-RAY DIFFRACTION100
1.472-1.51180.15021640.09272653X-RAY DIFFRACTION100
1.5118-1.55620.12391450.09722655X-RAY DIFFRACTION100
1.5562-1.60640.12791390.09432684X-RAY DIFFRACTION100
1.6064-1.66380.13231400.09392679X-RAY DIFFRACTION100
1.6638-1.73030.13761280.10192681X-RAY DIFFRACTION100
1.7303-1.8090.12671330.10672681X-RAY DIFFRACTION100
1.809-1.90430.14321400.11982680X-RAY DIFFRACTION100
1.9043-2.02350.15911660.12882653X-RAY DIFFRACTION100
2.0235-2.17940.16111400.13132679X-RAY DIFFRACTION100
2.1794-2.39830.13521590.12882675X-RAY DIFFRACTION100
2.3983-2.74420.15881290.14552709X-RAY DIFFRACTION100
2.7442-3.45320.16271460.15232681X-RAY DIFFRACTION100
3.4532-17.72510.17771340.16032690X-RAY DIFFRACTION98

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