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- PDB-7ey3: Double cysteine mutations in T1 lipase -

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Basic information

Entry
Database: PDB / ID: 7ey3
TitleDouble cysteine mutations in T1 lipase
ComponentsThermostable lipase
KeywordsHYDROLASE / disulphide bond / cysteine / lipase / site-directed mutagenesis / STRUCTURAL PROTEIN
Function / homologytriacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / extracellular region / metal ion binding / triacylglycerol lipase
Function and homology information
Biological speciesGeobacillus zalihae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsHamdan, S.H. / Leow, T.C. / Yahaya, N.M. / Ali, M.S.M. / Jonet, M.A. / Mohamad Aris, S.N.A. / Maiangwa, J.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2023
Title: Knotting terminal ends of mutant T1 lipase with disulfide bond improved structure rigidity and stability.
Authors: Hamdan, S.H. / Maiangwa, J. / Nezhad, N.G. / Ali, M.S.M. / Normi, Y.M. / Shariff, F.M. / Rahman, R.N.Z.R.A. / Leow, T.C.
History
DepositionMay 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 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
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermostable lipase
B: Thermostable lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,80210
Polymers86,4742
Non-polymers3288
Water6,233346
1
A: Thermostable lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4015
Polymers43,2371
Non-polymers1644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area14740 Å2
MethodPISA
2
B: Thermostable lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4015
Polymers43,2371
Non-polymers1644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.174, 81.496, 100.046
Angle α, β, γ (deg.)90.000, 96.940, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-634-

HOH

21B-637-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thermostable lipase


Mass: 43237.191 Da / Num. of mol.: 2 / Mutation: S2C, A384C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus zalihae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q842J9, triacylglycerol lipase

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Non-polymers , 5 types, 354 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.5M Sodium chloride, 0.1M Sodium citrate dihydrate pH 5.6, 2 % Ethylene imine polymer

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: CCD / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.04→40 Å / Num. obs: 59606 / % possible obs: 99.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.39 Å2 / CC1/2: 0.861 / Net I/σ(I): 16
Reflection shellResolution: 2.04→2.08 Å / Num. unique obs: 107633 / CC1/2: 0.886

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
DENZOdata reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dsn

2dsn


Resolution: 2.04→33.46 Å / SU ML: 0.2283 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2215 1998 3.36 %
Rwork0.1879 57543 -
obs0.189 59541 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.92 Å2
Refinement stepCycle: LAST / Resolution: 2.04→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 8 346 6462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00746276
X-RAY DIFFRACTIONf_angle_d0.88468536
X-RAY DIFFRACTIONf_chiral_restr0.0515894
X-RAY DIFFRACTIONf_plane_restr0.00541124
X-RAY DIFFRACTIONf_dihedral_angle_d16.003862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.090.28131370.21783942X-RAY DIFFRACTION95.84
2.09-2.150.24251380.20653989X-RAY DIFFRACTION96.92
2.15-2.210.28671410.22294047X-RAY DIFFRACTION97.9
2.21-2.280.25351410.23554069X-RAY DIFFRACTION98.78
2.28-2.360.28721420.21364096X-RAY DIFFRACTION99.44
2.36-2.460.22471440.19654132X-RAY DIFFRACTION99.49
2.46-2.570.23451440.20314137X-RAY DIFFRACTION99.63
2.57-2.710.24511420.20994114X-RAY DIFFRACTION99.7
2.71-2.870.28341440.21934146X-RAY DIFFRACTION99.79
2.87-3.10.26281430.21984125X-RAY DIFFRACTION99.93
3.1-3.410.21551450.19474159X-RAY DIFFRACTION100
3.41-3.90.19151440.16134155X-RAY DIFFRACTION99.95
3.9-4.910.15021450.13454179X-RAY DIFFRACTION99.95
4.91-33.460.17581480.15224253X-RAY DIFFRACTION99.91

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