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- PDB-4ke9: Crystal structure of Monoglyceride lipase from Bacillus sp. H257 ... -

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Basic information

Entry
Database: PDB / ID: 4ke9
TitleCrystal structure of Monoglyceride lipase from Bacillus sp. H257 in complex with an 1-stearyol glycerol analogue
ComponentsThermostable monoacylglycerol lipase
KeywordsHYDROLASE / alpha/beta hydrolase fold / 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
hexadecyl hydrogen (R)-(3-azidopropyl)phosphonate / Thermostable monoacylglycerol lipase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 1.3Oct 30, 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.pdbx_leaving_atom_flag / _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)118,9278
Polymers117,3694
Non-polymers1,5584
Water5,459303
1
A: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7322
Polymers29,3421
Non-polymers3901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7322
Polymers29,3421
Non-polymers3901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7322
Polymers29,3421
Non-polymers3901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7322
Polymers29,3421
Non-polymers3901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.857, 80.287, 85.712
Angle α, β, γ (deg.)90.00, 100.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thermostable monoacylglycerol lipase / MGLP


Mass: 29342.332 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-1R1 / hexadecyl hydrogen (R)-(3-azidopropyl)phosphonate


Mass: 389.513 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H40N3O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 0.1 M citric acid pH 5.0 and 22% PEG 3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2012
RadiationMonochromator: channel-cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→43.661 Å / Num. all: 48702 / Num. obs: 48702 / % possible obs: 93.2 % / Redundancy: 7 % / Rsym value: 0.139 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.2-2.324.80.5570.90.557168.4
2.32-2.465.60.3181.70.318185.8
2.46-2.637.20.2532.10.253199.7
2.63-2.847.60.2022.90.2021100
2.84-3.117.60.1543.80.1541100
3.11-3.487.60.1334.10.1331100
3.48-4.027.60.1344.30.1341100
4.02-4.927.60.1065.20.1061100
4.92-6.967.40.1035.40.1031100
6.96-43.6616.80.0837.10.083194.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.66 Å
Translation2.5 Å43.66 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.661 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / σ(F): 1.39 / Phase error: 32.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 2492 5.13 %
Rwork0.2228 --
obs0.2248 48678 92.51 %
all-48555 -
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--10.464 Å20 Å21.0079 Å2
2--20.7308 Å2-0 Å2
3----10.2669 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7615 0 100 303 8018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037907
X-RAY DIFFRACTIONf_angle_d0.8410740
X-RAY DIFFRACTIONf_dihedral_angle_d12.5862836
X-RAY DIFFRACTIONf_chiral_restr0.0431191
X-RAY DIFFRACTIONf_plane_restr0.0041378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.3956990.3341966X-RAY DIFFRACTION60
2.225-2.25120.49211230.43851990X-RAY DIFFRACTION62
2.2512-2.27870.37711330.30032149X-RAY DIFFRACTION67
2.2787-2.30750.32941070.24222304X-RAY DIFFRACTION70
2.3075-2.33790.33141530.23142397X-RAY DIFFRACTION75
2.3379-2.36990.26751340.23392524X-RAY DIFFRACTION79
2.3699-2.40380.33831540.23492783X-RAY DIFFRACTION85
2.4038-2.43960.27971250.23712951X-RAY DIFFRACTION90
2.4396-2.47770.25771650.23793060X-RAY DIFFRACTION95
2.4777-2.51840.29591660.22893237X-RAY DIFFRACTION99
2.5184-2.56180.25741490.22513224X-RAY DIFFRACTION100
2.5618-2.60840.29071880.22463243X-RAY DIFFRACTION100
2.6084-2.65850.29281540.22243273X-RAY DIFFRACTION100
2.6585-2.71280.24321760.22213202X-RAY DIFFRACTION100
2.7128-2.77180.28561750.2223258X-RAY DIFFRACTION100
2.7718-2.83620.26741590.22613244X-RAY DIFFRACTION100
2.8362-2.90710.25491910.2333198X-RAY DIFFRACTION100
2.9071-2.98570.30582020.23823244X-RAY DIFFRACTION100
2.9857-3.07360.3151830.24163262X-RAY DIFFRACTION100
3.0736-3.17270.27332010.23573190X-RAY DIFFRACTION100
3.1727-3.28610.29381840.24273212X-RAY DIFFRACTION100
3.2861-3.41760.25262020.23193192X-RAY DIFFRACTION100
3.4176-3.57310.27161620.22453277X-RAY DIFFRACTION100
3.5731-3.76140.25961670.21733227X-RAY DIFFRACTION100
3.7614-3.99690.19841850.20083244X-RAY DIFFRACTION100
3.9969-4.30520.25211600.1953248X-RAY DIFFRACTION100
4.3052-4.7380.22681950.18333212X-RAY DIFFRACTION100
4.738-5.42250.21271650.20133241X-RAY DIFFRACTION100
5.4225-6.82760.21391490.21123263X-RAY DIFFRACTION100
6.8276-43.66950.20931510.19743074X-RAY DIFFRACTION94

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