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- PDB-6eic: Crystal structure of Rv0183, a Monoglyceride Lipase from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 6eic
TitleCrystal structure of Rv0183, a Monoglyceride Lipase from Mycobacterium Tuberculosis
ComponentsMycobacterium Tuberculosis Monoglyceride Lipase
KeywordsHYDROLASE / Monoglycerid Lipase / Lipase / Alpha/Beta hydrolase
Function / homology
Function and homology information


glycerolipid catabolic process / acylglycerol lipase / lipase activity / monoacylglycerol lipase activity / peptidoglycan-based cell wall / symbiont-mediated activation of host apoptosis / extracellular region / membrane / plasma membrane
Similarity search - Function
: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
NITRATE ION / Monoacylglycerol lipase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAschauer, P. / Pavkov-Keller, T. / Oberer, M.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP 24857 Austria
CitationJournal: Sci Rep / Year: 2018
Title: The crystal structure of monoacylglycerol lipase from M. tuberculosis reveals the basis for specific inhibition.
Authors: Aschauer, P. / Zimmermann, R. / Breinbauer, R. / Pavkov-Keller, T. / Oberer, M.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Mycobacterium Tuberculosis Monoglyceride Lipase
A: Mycobacterium Tuberculosis Monoglyceride Lipase
B: Mycobacterium Tuberculosis Monoglyceride Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4088
Polymers90,8963
Non-polymers5135
Water8,269459
1
C: Mycobacterium Tuberculosis Monoglyceride Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5133
Polymers30,2991
Non-polymers2142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Mycobacterium Tuberculosis Monoglyceride Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4172
Polymers30,2991
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Mycobacterium Tuberculosis Monoglyceride Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4793
Polymers30,2991
Non-polymers1802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.825, 85.825, 196.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11C-517-

HOH

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Components

#1: Protein Mycobacterium Tuberculosis Monoglyceride Lipase


Mass: 30298.533 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv0183 / Production host: Escherichia coli (E. coli) / References: UniProt: O07427
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.03M sodium nitrate, 0.03M di-sodium hydrogenphosphate, 0.03M ammonium sulfate, 0.1M MOPS/HEPES, 12% 2-Methyl 2,4 pentandiol, 12% PEG1000, 12% PEG3350. Microseeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.8→49.209 Å / Num. obs: 77304 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.035 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4549 / CC1/2: 0.734 / Rpim(I) all: 0.307 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SCALAdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.209 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.91
RfactorNum. reflection% reflection
Rfree0.251 3805 4.93 %
Rwork0.2213 --
obs0.2227 77233 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→49.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6317 0 33 459 6809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036478
X-RAY DIFFRACTIONf_angle_d1.018841
X-RAY DIFFRACTIONf_dihedral_angle_d22.3242356
X-RAY DIFFRACTIONf_chiral_restr0.0431020
X-RAY DIFFRACTIONf_plane_restr0.0041161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8002-1.83130.43731630.3713689X-RAY DIFFRACTION96
1.8313-1.86460.33811690.32923646X-RAY DIFFRACTION96
1.8646-1.90040.33971680.30883642X-RAY DIFFRACTION96
1.9004-1.93920.31381900.28993640X-RAY DIFFRACTION95
1.9392-1.98130.28091660.26073659X-RAY DIFFRACTION96
1.9813-2.02740.31882100.25823634X-RAY DIFFRACTION95
2.0274-2.07810.29241790.25153634X-RAY DIFFRACTION95
2.0781-2.13420.27951890.24283649X-RAY DIFFRACTION95
2.1342-2.1970.25862120.2383664X-RAY DIFFRACTION95
2.197-2.26780.27312090.23143620X-RAY DIFFRACTION95
2.2678-2.34880.2711880.23313640X-RAY DIFFRACTION95
2.3488-2.44280.26632060.2293682X-RAY DIFFRACTION95
2.4428-2.55380.25071790.22463643X-RAY DIFFRACTION95
2.5538-2.68830.24632050.22573657X-RAY DIFFRACTION95
2.6883-2.85650.26312010.21893667X-RAY DIFFRACTION95
2.8565-3.07660.24541910.20923674X-RAY DIFFRACTION95
3.0766-3.38550.21562010.19943673X-RAY DIFFRACTION95
3.3855-3.87360.20771700.18143706X-RAY DIFFRACTION96
3.8736-4.87370.21112010.17363716X-RAY DIFFRACTION95
4.8737-24.02910.22842080.21033824X-RAY DIFFRACTION95

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