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- PDB-7buk: T1 lipase mutant - 5M (D43E/T118N/E226D/E250L/N304E) -

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Basic information

Entry
Database: PDB / ID: 7buk
TitleT1 lipase mutant - 5M (D43E/T118N/E226D/E250L/N304E)
ComponentsLipase
KeywordsHYDROLASE / lipase / mutation / triglycerides
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesGeobacillus zalihae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.644 Å
AuthorsIshak, S.N.H. / Rahman, R.N.Z.R.A. / Ali, M.S.M. / Leow, A.T.C. / Kamarudin, N.H.A.
CitationJournal: Plos One / Year: 2021
Title: Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae.
Authors: Ishak, S.N.H. / Kamarudin, N.H.A. / Ali, M.S.M. / Leow, A.T.C. / Shariff, F.M. / Rahman, R.N.Z.R.A.
History
DepositionApr 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0386
Polymers90,8272
Non-polymers2114
Water3,297183
1
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5193
Polymers45,4141
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area14930 Å2
MethodPISA
2
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5193
Polymers45,4141
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.592, 81.269, 99.522
Angle α, β, γ (deg.)90.000, 97.320, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-578-

HOH

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Components

#1: Protein Lipase


Mass: 45413.684 Da / Num. of mol.: 2 / Mutation: D43E/T118N/E226D/E250L/N304E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus zalihae (bacteria) / Plasmid: pLysS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: triacylglycerol lipase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThis is D43E/T118N/E226D/E250L/N304E mutant. And 18 N-terminal residues (MSPISRHHHHHHLVPRGS) are ...This is D43E/T118N/E226D/E250L/N304E mutant. And 18 N-terminal residues (MSPISRHHHHHHLVPRGS) are expression tags.

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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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.5, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jun 19, 2019 / Details: DEXTRIS 200K
RadiationMonochromator: cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.65→40 Å / Num. obs: 24822 / % possible obs: 90.9 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 14
Reflection shellResolution: 2.65→2.7 Å / Rmerge(I) obs: 0.129 / Num. unique obs: 38251

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DSN

2dsn


Resolution: 2.644→35.1 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.856 / SU B: 11.524 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.376
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1188 4.8 %RANDOM
Rwork0.1844 ---
obs0.188 23631 90.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.42 Å2 / Biso mean: 15.927 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20.9 Å2
2---1.83 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 2.644→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6112 0 4 183 6299
Biso mean--32.65 10.42 -
Num. residues----774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136280
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175564
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.6428540
X-RAY DIFFRACTIONr_angle_other_deg1.2471.57312848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3245772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.58421.148366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49915954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4311552
X-RAY DIFFRACTIONr_chiral_restr0.0690.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021478
LS refinement shellResolution: 2.644→2.712 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 77 -
Rwork0.266 1505 -
all-1582 -
obs--78.32 %

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