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- PDB-7e0n: Crystal structure of Monoacylglycerol Lipase chimera -

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Basic information

Entry
Database: PDB / ID: 7e0n
TitleCrystal structure of Monoacylglycerol Lipase chimera
ComponentsThermostable monoacylglycerol lipase,Lipase
KeywordsHYDROLASE / Monoacylglycerol Lipase
Function / homologyEsterase/lipase / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Lipase
Function and homology information
Biological speciesGeobacillus sp. 12AMOR1 (bacteria)
Bacillus oceanisediminis 2691 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLan, D.M.
CitationJournal: To Be Published
Title: Crystal structure of Monoacylglycerol Lipase chimera
Authors: Lan, D.M. / Wang, Y.H.
History
DepositionJan 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Thermostable monoacylglycerol lipase,Lipase
B: Thermostable monoacylglycerol lipase,Lipase
C: Thermostable monoacylglycerol lipase,Lipase
D: Thermostable monoacylglycerol lipase,Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5368
Polymers116,1684
Non-polymers3684
Water25,3831409
1
A: Thermostable monoacylglycerol lipase,Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1342
Polymers29,0421
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thermostable monoacylglycerol lipase,Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1342
Polymers29,0421
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thermostable monoacylglycerol lipase,Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1342
Polymers29,0421
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thermostable monoacylglycerol lipase,Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1342
Polymers29,0421
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.798, 99.854, 207.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-661-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 3 or resid 5...
d_2ens_1(chain "B" and (resid 1 through 3 or resid 5...
d_3ens_1(chain "C" and (resid 1 through 3 or resid 5...
d_4ens_1(chain "D" and (resid 1 through 3 or resid 5...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METGLUA1 - 3
d_12ens_1TYRTHRA5 - 69
d_13ens_1GLNASNA72 - 87
d_14ens_1CYSILEA89 - 114
d_15ens_1GLYVALA116 - 220
d_16ens_1LEULEUA222 - 243
d_17ens_1PHETHRA245 - 252
d_18ens_1GOLGOLB
d_21ens_1METGLUC1 - 3
d_22ens_1TYRTHRC6 - 70
d_23ens_1GLNASNC72 - 87
d_24ens_1CYSILEC89 - 114
d_25ens_1GLYVALC117 - 221
d_26ens_1LEULEUC223 - 244
d_27ens_1PHETHRC246 - 253
d_28ens_1GOLGOLD
d_31ens_1METGLUE1 - 3
d_32ens_1TYRTHRE5 - 69
d_33ens_1GLNASNE72 - 87
d_34ens_1CYSILEE89 - 114
d_35ens_1GLYVALE117 - 221
d_36ens_1LEULEUE224 - 245
d_37ens_1PHETHRE248 - 255
d_38ens_1GOLGOLF
d_41ens_1METGLUG1 - 3
d_42ens_1TYRTHRG5 - 69
d_43ens_1GLNASNG71 - 86
d_44ens_1CYSILEG89 - 114
d_45ens_1GLYVALG117 - 221
d_46ens_1LEULEUG223 - 244
d_47ens_1PHETHRG246 - 253
d_48ens_1GOLGOLH

NCS oper:
IDCodeMatrixVector
1given(0.999301270651, 0.0347342997903, -0.0138021336231), (0.0353341101025, -0.99832122001, 0.0458938159356), (-0.0121848733161, -0.0463494346885, -0.998850969247)31.8499006042, 50.0876302799, 104.867800434
2given(-0.999693035568, -0.018196331213, -0.0168145224825), (-0.0174529014124, 0.998907495011, -0.0433498863066), (0.0175849614221, -0.0430431172302, -0.998918444715)24.4217619914, 1.23177655939, 52.551742878
3given(-0.999979986329, -0.00483529941096, -0.0040800516212), (0.00485960892994, -0.999970374724, -0.00596941159136), (-0.0040510668562, -0.00598911957682, 0.99997385931)56.2050059208, 51.4375652517, 52.0328456754

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Components

#1: Protein
Thermostable monoacylglycerol lipase,Lipase


Mass: 29042.029 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus sp. 12AMOR1 (bacteria), (gene. exp.) Bacillus oceanisediminis 2691 (bacteria)
Gene: A361_02165 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A160MIM0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1409 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe sequence of residue 1-160 is GenBank entry AKM18206.1.

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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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: potassium phosphate dibasic, sodium phosphate monobasic, imidazole/hydrochloric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 115284 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 19.83 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.054 / Net I/σ(I): 19.5
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 4 / Num. unique obs: 5671 / Rpim(I) all: 0.234 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XKS

5xks


Resolution: 1.85→23.63 Å / SU ML: 0.1333 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.0468
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1779 1904 1.76 %
Rwork0.1548 106059 -
obs0.1552 107963 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.05 Å2
Refinement stepCycle: LAST / Resolution: 1.85→23.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7712 0 24 1409 9145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017979
X-RAY DIFFRACTIONf_angle_d1.149410832
X-RAY DIFFRACTIONf_chiral_restr0.1791219
X-RAY DIFFRACTIONf_plane_restr0.0081400
X-RAY DIFFRACTIONf_dihedral_angle_d14.04191087
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.746903897188
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.568979785014
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.660131451096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.2721180.20866236X-RAY DIFFRACTION78.52
1.9-1.950.20211190.19486974X-RAY DIFFRACTION87.22
1.95-2.010.18911310.18367305X-RAY DIFFRACTION91.51
2.01-2.070.18631390.16557602X-RAY DIFFRACTION95.05
2.07-2.140.17891380.16167712X-RAY DIFFRACTION96.39
2.14-2.230.19791390.15937766X-RAY DIFFRACTION96.56
2.23-2.330.19921410.15777794X-RAY DIFFRACTION96.89
2.33-2.450.19521390.1587758X-RAY DIFFRACTION97.04
2.45-2.610.16581400.1577871X-RAY DIFFRACTION97.27
2.61-2.810.17951420.15417929X-RAY DIFFRACTION98.02
2.81-3.090.17991440.1537953X-RAY DIFFRACTION98.01
3.09-3.540.18061430.14768026X-RAY DIFFRACTION98.79
3.54-4.450.15491450.13228030X-RAY DIFFRACTION97.59
4.45-23.630.15591260.15387103X-RAY DIFFRACTION83.14

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