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- PDB-7ozm: Crystal Structure of mtbMGL K74A (Closed Cap Conformation) -

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Basic information

Entry
Database: PDB / ID: 7ozm
TitleCrystal Structure of mtbMGL K74A (Closed Cap Conformation)
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
ISOPROPYL ALCOHOL / Monoacylglycerol lipase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6782
Polymers33,6181
Non-polymers601
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint4 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.500, 82.240, 90.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Monoacylglycerol lipase / MGL


Mass: 33618.047 Da / Num. of mol.: 1
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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15 % 2-propanol, 24 % PEG 3350, 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, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.15→39.77 Å / Num. obs: 16663 / % possible obs: 97.22 % / Redundancy: 3.3 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.086 / Rrim(I) all: 0.167 / Net I/σ(I): 7.27
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 1655 / CC1/2: 0.578 / CC star: 0.856 / Rpim(I) all: 0.462 / Rrim(I) all: 0.889 / % possible all: 97.93

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6eic

6eic


Resolution: 2.15→39.77 Å / SU ML: 0.3201 / Cross valid method: FREE R-VALUE / σ(F): 0.83 / Phase error: 26.7245
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25 2964 9.99 %
Rwork0.195 26697 -
obs0.2005 16657 93.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.97 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 4 133 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742170
X-RAY DIFFRACTIONf_angle_d0.8582964
X-RAY DIFFRACTIONf_chiral_restr0.0529343
X-RAY DIFFRACTIONf_plane_restr0.0091392
X-RAY DIFFRACTIONf_dihedral_angle_d5.2328311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.35521410.30071273X-RAY DIFFRACTION92.9
2.19-2.220.35991460.29861295X-RAY DIFFRACTION93.94
2.22-2.260.30091420.29061253X-RAY DIFFRACTION90.88
2.26-2.310.36091420.27281258X-RAY DIFFRACTION95.04
2.31-2.360.30851440.26441329X-RAY DIFFRACTION95.34
2.36-2.410.31231440.25661295X-RAY DIFFRACTION95.87
2.41-2.460.3221420.25431285X-RAY DIFFRACTION95.9
2.46-2.520.28741450.24791312X-RAY DIFFRACTION94.3
2.52-2.590.33561420.23881269X-RAY DIFFRACTION94.95
2.59-2.670.321460.2381295X-RAY DIFFRACTION93.27
2.67-2.750.30651340.23281232X-RAY DIFFRACTION90.58
2.75-2.850.27571420.21281310X-RAY DIFFRACTION96.1
2.85-2.970.27841460.21071282X-RAY DIFFRACTION94.76
2.97-3.10.28251430.20341303X-RAY DIFFRACTION94.76
3.1-3.270.29671450.19641267X-RAY DIFFRACTION93.7
3.27-3.470.22061380.17611264X-RAY DIFFRACTION92.42
3.47-3.740.22651380.15611250X-RAY DIFFRACTION91.38
3.74-4.110.19091450.15041273X-RAY DIFFRACTION92.98
4.11-4.710.17431290.13111224X-RAY DIFFRACTION89.9
4.71-5.930.18291290.151217X-RAY DIFFRACTION88.32
5.93-39.770.17711410.15951211X-RAY DIFFRACTION88.89

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