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- PDB-7v6d: Structure of lipase B from Lasiodiplodia theobromae -

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Basic information

Entry
Database: PDB / ID: 7v6d
TitleStructure of lipase B from Lasiodiplodia theobromae
ComponentsLipase B
KeywordsHYDROLASE / alpha/beta-hydrolases
Function / homology: / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Lipase B
Function and homology information
Biological speciesLasiodiplodia theobromae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsXue, B. / Zhang, H.F. / Nguyen, G.K.T. / Yew, W.S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: Int J Mol Sci / Year: 2021
Title: A Novel Lipase from Lasiodiplodia theobromae Efficiently Hydrolyses C8-C10 Methyl Esters for the Preparation of Medium-Chain Triglycerides' Precursors.
Authors: Ng, A.M.J. / Yang, R. / Zhang, H. / Xue, B. / Yew, W.S. / Nguyen, G.K.T.
History
DepositionAug 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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

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Assembly

Deposited unit
A: Lipase B
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6585
Polymers90,1542
Non-polymers5053
Water2,126118
1
A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5413
Polymers45,0771
Non-polymers4642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-5 kcal/mol
Surface area13810 Å2
MethodPISA
2
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1172
Polymers45,0771
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.428, 162.639, 166.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Lipase B


Mass: 45076.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lasiodiplodia theobromae (fungus) / Gene: LIPB, DBV05_g2145 / Plasmid: pPIC9K / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: A0A5N5DNA6
#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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.46 Å3/Da / Density % sol: 49.98 % / Mosaicity: 0.12 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 60% MPD, 100 mM NaOAc, pH 4.6, 10 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.5→29.7 Å / Num. obs: 31233 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 37.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.053 / Rrim(I) all: 0.198 / Net I/σ(I): 11.9 / Num. measured all: 425607 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.6141.2024851734670.8540.3321.2472.2100
9.01-29.713.20.04896157310.9990.0140.0544.897.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IDY

6idy


Resolution: 2.5→29.7 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 1554 4.98 %
Rwork0.1922 29663 -
obs0.1948 31217 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.1 Å2 / Biso mean: 43.7346 Å2 / Biso min: 20.06 Å2
Refinement stepCycle: final / Resolution: 2.5→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5422 0 30 118 5570
Biso mean--48.06 41.42 -
Num. residues----733
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.580.29471500.242326492799
2.58-2.670.37561500.241326432793
2.67-2.780.32881410.234626472788
2.78-2.910.29621400.213826612801
2.91-3.060.28851490.215926562805
3.06-3.250.24361510.204726872838
3.25-3.50.2171410.186326582799
3.5-3.850.22751190.174627312850
3.85-4.410.1951450.158827032848
4.41-5.550.21111370.179127572894
5.55-29.70.231310.191928713002

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