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- PDB-6unv: Crystal structure of a methanol tolerant lipase/esterase from the... -

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Basic information

Entry
Database: PDB / ID: 6unv
TitleCrystal structure of a methanol tolerant lipase/esterase from the fungus Rasamsonia emersonii
ComponentsLipase
KeywordsHYDROLASE / Lipase / esterase / macaw oil hydrolysis / methanol tolerant
Function / homology
Function and homology information


lipid catabolic process
Similarity search - Function
Mono-/di-acylglycerol lipase, N-terminal / Lipase 3 N-terminal region / : / Fungal lipase-like domain / Lipase (class 3) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRasamsonia emersonii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVieira, P.S. / Milan, N. / Murakami, M.T. / Zanphorlin, L.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)19/08855-1 Brazil
Sao Paulo Research Foundation (FAPESP)15/26982-0 Brazil
CitationJournal: Front Bioeng Biotechnol / Year: 2020
Title: A Novel Fungal Lipase With Methanol Tolerance and Preference for Macaw Palm Oil.
Authors: Rade, L.L. / da Silva, M.N.P. / Vieira, P.S. / Milan, N. / de Souza, C.M. / de Melo, R.R. / Klein, B.C. / Bonomi, A. / de Castro, H.F. / Murakami, M.T. / Zanphorlin, L.M.
History
DepositionOct 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase


Theoretical massNumber of molelcules
Total (without water)31,7781
Polymers31,7781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.000, 91.000, 116.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Lipase


Mass: 31777.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rasamsonia emersonii (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F4YFS6
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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 100 mmol/L MgCl2, 20% PEG 8000, 20% PEG 400, 100 mmol/L Tris buffer pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2018
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.55→35.587 Å / Num. obs: 8208 / % possible obs: 99.7 % / Redundancy: 19.69 % / CC1/2: 0.99 / Rrim(I) all: 0.29 / Net I/σ(I): 8.94
Reflection shellResolution: 2.55→2.7 Å / Num. unique obs: 1276 / CC1/2: 0.36 / % possible all: 98.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_3139refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHENIXmodel building
PHASERphasing
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ch8

5ch8


Resolution: 3→35.587 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 34.39
RfactorNum. reflection% reflection
Rfree0.3287 513 10 %
Rwork0.2791 --
obs0.284 5129 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.52 Å2 / Biso min: 42.72 Å2
Refinement stepCycle: final / Resolution: 3→35.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 0 0 1980
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3-3.30120.39141241117
3.3012-3.77840.40071271138
3.7784-4.75860.30361270.27021140
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)
12.2048-1.2029-0.46287.6276-3.00496.4821-0.2789-0.15990.08681.04280.47960.7781-0.8081-0.8989-0.19690.51840.03820.01690.45430.18230.8556-5.3175-24.3714-3.9701
22.8252-2.3802-0.4444.4238-1.52983.6182-0.43130.45520.9882-0.20850.67250.961-0.6193-0.324-0.3840.6779-0.0745-0.06350.40980.15160.74710.9884-17.1062-6.9661
32.46281.3127-0.91292.0428-0.56124.09830.0478-0.00830.1446-0.2452-0.0425-0.696-0.22760.79012.25530.4333-0.07220.14630.70880.29091.536913.5002-23.6311-11.1804
41.03351.3126-0.04013.171-1.82962.10070.2250.2806-0.2352-1.1476-0.8094-1.16970.38070.39630.16970.41810.06830.17070.4790.29171.05244.8569-28.3195-12.332
51.73770.62230.12420.269-0.28152.37520.45690.71510.3695-2.1441-1.0226-1.02890.53310.29080.41790.96640.33880.30550.66890.16121.04622.5669-17.2276-21.326
62.3156-0.84880.10615.7745-1.35472.96870.66940.57590.4561-0.92790.03211.29730.37-0.2812-0.15280.7420.1626-0.01020.41370.2510.9934-9.4419-12.892-18.3645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 101 )A31 - 101
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 126 )A102 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 165 )A127 - 165
4X-RAY DIFFRACTION4chain 'A' and (resid 166 through 196 )A166 - 196
5X-RAY DIFFRACTION5chain 'A' and (resid 197 through 249 )A197 - 249
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 301 )A250 - 301

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