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- PDB-7p0y: Crystal Structure of mtbMGL K74A (Substrate Analog Complex) -

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Basic information

Entry
Database: PDB / ID: 7p0y
TitleCrystal Structure of mtbMGL K74A (Substrate Analog Complex)
ComponentsMonoacylglycerol lipase
KeywordsHYDROLASE / Mycobacterium tuberculosis / monoacylglycerol lipase
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
1-[butyl(fluoranyl)phosphoryl]oxyhexadecane / Monoacylglycerol lipase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGrininger, C. / Aschauer, P. / Pavkov-Keller, T. / Oberer, M.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP24857 Austria
Austrian Science FundP29432 Austria
CitationJournal: Biomolecules / Year: 2021
Title: Structural Changes in the Cap of Rv0183/mtbMGL Modulate the Shape of the Binding Pocket.
Authors: Grininger, C. / Leypold, M. / Aschauer, P. / Pavkov-Keller, T. / Riegler-Berket, L. / Breinbauer, R. / Oberer, M.
History
DepositionJun 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monoacylglycerol lipase
B: Monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0174
Polymers61,2882
Non-polymers7292
Water2,540141
1
A: Monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0082
Polymers30,6441
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0082
Polymers30,6441
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.690, 82.603, 93.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Monoacylglycerol lipase / MGL


Mass: 30643.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0183, LH57_01015 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O07427, acylglycerol lipase
#2: Chemical ChemComp-4E0 / 1-[butyl(fluoranyl)phosphoryl]oxyhexadecane


Mass: 364.518 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H42FO2P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30 % PEG300, 125 mM Calcium acetate, 100 mM Tris-HCl pH 8.5, 10 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.25→40.78 Å / Num. obs: 28192 / % possible obs: 99.65 % / Redundancy: 5.2 % / Biso Wilson estimate: 36.18 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.071 / Rrim(I) all: 0.165 / Net I/σ(I): 20.99
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 2766 / CC1/2: 0.77 / CC star: 0.933 / Rpim(I) all: 0.35 / Rrim(I) all: 0.802 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EIC

6eic


Resolution: 2.25→40.78 Å / SU ML: 0.3809 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.8137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2951 3751 7.11 %
Rwork0.2534 49016 -
obs0.2564 28118 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.6 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 46 141 4373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274326
X-RAY DIFFRACTIONf_angle_d0.60745892
X-RAY DIFFRACTIONf_chiral_restr0.0421676
X-RAY DIFFRACTIONf_plane_restr0.0052775
X-RAY DIFFRACTIONf_dihedral_angle_d18.76231594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.34531420.34241838X-RAY DIFFRACTION99.4
2.28-2.310.34881370.32081805X-RAY DIFFRACTION98.93
2.31-2.340.38281310.31491780X-RAY DIFFRACTION97.25
2.34-2.370.3451380.31071830X-RAY DIFFRACTION98.45
2.37-2.410.37051340.30191808X-RAY DIFFRACTION99.03
2.41-2.450.34751420.30771804X-RAY DIFFRACTION99.39
2.45-2.490.36331420.32991814X-RAY DIFFRACTION99.59
2.49-2.530.34861420.3141810X-RAY DIFFRACTION98.89
2.53-2.580.36811400.2931806X-RAY DIFFRACTION99.54
2.58-2.630.43891410.29441816X-RAY DIFFRACTION99.29
2.63-2.680.30321420.3011827X-RAY DIFFRACTION99.29
2.68-2.740.35351410.29221804X-RAY DIFFRACTION99.79
2.74-2.80.39121410.27811844X-RAY DIFFRACTION99.55
2.8-2.870.38071430.29051833X-RAY DIFFRACTION99.75
2.87-2.950.33391360.29091824X-RAY DIFFRACTION99.24
2.95-3.030.40971350.29791764X-RAY DIFFRACTION97.69
3.03-3.130.29331410.31261832X-RAY DIFFRACTION99.35
3.13-3.240.37321350.25361829X-RAY DIFFRACTION99.44
3.24-3.370.31771400.25341813X-RAY DIFFRACTION99.34
3.37-3.530.2991380.25581822X-RAY DIFFRACTION99.64
3.53-3.710.31611430.24191836X-RAY DIFFRACTION99.85
3.71-3.950.28421380.22641827X-RAY DIFFRACTION99.75
3.95-4.250.26271350.21591805X-RAY DIFFRACTION98.93
4.25-4.680.24561430.20651796X-RAY DIFFRACTION98.93
4.68-5.350.19981370.20051823X-RAY DIFFRACTION99.39
5.35-6.740.21311370.2291822X-RAY DIFFRACTION99.24
6.74-40.780.20061370.2031804X-RAY DIFFRACTION98.23

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