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- PDB-7spr: Crystal structure of SMG1 mutant (G28C/P206C/Q34P/A37P/M176V/G177... -

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Basic information

Entry
Database: PDB / ID: 7spr
TitleCrystal structure of SMG1 mutant (G28C/P206C/Q34P/A37P/M176V/G177A/M294R/F278N)
ComponentsLIP1, secretory lipase (Family 3)
KeywordsHYDROLASE / SMG1
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lipid catabolic process / hydrolase activity / extracellular region / metal ion binding
Similarity search - Function
Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Secreted mono- and diacylglycerol lipase LIP1
Similarity search - Component
Biological speciesMalassezia globosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsLi, L.L. / Wang, Y.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Lipase SMG1 thermostability optimizing through protein design approach
Authors: Li, L.L. / Wang, Y.H.
History
DepositionNov 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: LIP1, secretory lipase (Family 3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3212
Polymers30,8971
Non-polymers4241
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.053, 48.996, 110.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein LIP1, secretory lipase (Family 3)


Mass: 30896.699 Da / Num. of mol.: 1 / Mutation: G28C,Q34P,A37P,M176V,G177A,P206C,F278N,M294R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malassezia globosa (strain ATCC MYA-4612 / CBS 7966) (fungus)
Strain: ATCC MYA-4612 / CBS 7966 / Gene: MGL_0797 / Production host: Komagataella phaffii (fungus) / References: UniProt: A8PUY1
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 150 mM potassium bromide, 30% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 37769 / % possible obs: 99.4 % / Redundancy: 12.6 % / Biso Wilson estimate: 17.82 Å2 / CC1/2: 0.992 / Net I/σ(I): 19.9
Reflection shellResolution: 1.79→1.84 Å / Num. unique obs: 1731 / CC1/2: 0.963

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.19.2_4158refinement
PHENIXphasing
HKL-3000data scaling
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UUE

3uue


Resolution: 1.79→25.14 Å / SU ML: 0.1522 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.9952
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.183 1897 5.02 %
Rwork0.1569 35872 -
obs0.1582 37769 79.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.07 Å2
Refinement stepCycle: LAST / Resolution: 1.79→25.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 28 225 2419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792265
X-RAY DIFFRACTIONf_angle_d0.92683080
X-RAY DIFFRACTIONf_chiral_restr0.0601333
X-RAY DIFFRACTIONf_plane_restr0.0075404
X-RAY DIFFRACTIONf_dihedral_angle_d7.3406320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.2614890.21111642X-RAY DIFFRACTION51.06
1.84-1.890.2292940.19361840X-RAY DIFFRACTION57.24
1.89-1.940.20341030.1781904X-RAY DIFFRACTION59.34
1.94-2.010.2143970.17871972X-RAY DIFFRACTION61.32
2.01-2.080.221160.17442030X-RAY DIFFRACTION63.85
2.08-2.160.21041160.16512319X-RAY DIFFRACTION71.83
2.16-2.260.14951410.14582581X-RAY DIFFRACTION81.06
2.26-2.380.19251570.15852932X-RAY DIFFRACTION90.88
2.38-2.530.2221600.15753019X-RAY DIFFRACTION94.42
2.53-2.720.16861840.15423172X-RAY DIFFRACTION99.17
2.72-30.16361700.15973179X-RAY DIFFRACTION98.94
3-3.430.20321650.15853102X-RAY DIFFRACTION96.51
3.43-4.320.14781530.13823098X-RAY DIFFRACTION96.3
4.32-25.140.18041520.15593082X-RAY DIFFRACTION96.14
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.84366044156-0.0745974615281-0.02891427454781.99126923812-0.6727924857271.305209574050.0508461700454-0.1606563789690.2051629081930.0967028504442-0.0682129475083-0.102906180065-0.114290101013-0.01820347182170.02265093982050.164831310627-0.0163661937001-0.005442540523680.0929446903201-0.01580897821040.10307055938323.77755896361.90127126634-16.1064741949
25.169711323160.5898763066330.1271824234165.62896012850.1907564746425.26445018868-0.0572009227625-0.6981793348720.4806055871440.6466346808170.4070773640550.645003980573-0.0719466169471-0.775235903806-0.23620669550.2520892902880.07915281019330.06807521299840.3427395136640.02300275129520.2902888971483.203559525924.07299111908-12.4902281508
33.85120738002-0.049804539131-0.5252463294323.48699219238-1.012879211021.683558132630.00156116637516-0.362308719341-0.4012572846640.346969066951-0.006408306328240.2988214946530.0189538309011-0.140441461829-0.04705448829630.135024678157-0.01658803515890.01140354466370.1639087941020.04562537972370.09031170725589.97660877199-11.3579276502-16.9248329917
43.6608813771-0.00228285311217-0.506667301021.62824857279-0.3430383113411.362347907780.0440624423554-0.5667939197820.08767155404680.238478510262-0.0275730293863-0.0724398036393-0.112930046450.0813590553686-0.01014301432350.138904107462-0.00734856923211-0.002763513862770.1306898305430.01646874965240.06602881944422.4860075823-3.76807610942-13.3907722718
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 56 )28 - 561 - 29
22chain 'A' and (resid 57 through 89 )57 - 8930 - 62
33chain 'A' and (resid 90 through 164 )90 - 16463 - 137
44chain 'A' and (resid 165 through 304 )165 - 304138 - 277

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