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- PDB-2z5g: Crystal structure of T1 lipase F16L mutant -

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Basic information

Entry
Database: PDB / ID: 2z5g
TitleCrystal structure of T1 lipase F16L mutant
ComponentsThermostable lipase
KeywordsHYDROLASE / lipase / cation-pi interaction
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
: / Lipase-like, C-terminal domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
triacylglycerol lipase
Similarity search - Component
Biological speciesGeobacillus zalihae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMatsumura, H. / Yamamoto, T. / Inoue, T. / Kai, Y.
CitationJournal: Proteins / Year: 2007
Title: Novel cation-pi interaction revealed by crystal structure of thermoalkalophilic lipase
Authors: Matsumura, H. / Yamamoto, T. / Leow, T.C. / Mori, T. / Salleh, A.B. / Basri, M. / Inoue, T. / Kai, Y. / Rahman, R.N.Z.R.A.
History
DepositionJul 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,5928
Polymers86,3102
Non-polymers2826
Water12,358686
1
A: Thermostable lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2964
Polymers43,1551
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thermostable lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2964
Polymers43,1551
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.784, 81.111, 99.475
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2205-

HOH

21B-2411-

HOH

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Components

#1: Protein Thermostable lipase / T1 lipase


Mass: 43155.051 Da / Num. of mol.: 2 / Fragment: UNP residues 30-416 / Mutation: F16L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus zalihae (bacteria) / Plasmid: pGEX/T1S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q842J9, triacylglycerol lipase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O

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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: 54.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.5M NaCl, 0.1M KH2PO4, 0.1M NaH2PO4, 0.1M MES buffer, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→32.3 Å / Num. obs: 83050 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.344 / Num. unique all: 8179 / % possible all: 95.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DSN

2dsn


Resolution: 1.8→32.25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 393813.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4018 5.1 %RANDOM
Rwork0.196 ---
obs0.196 79386 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1305 Å2 / ksol: 0.374752 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.5 Å20 Å21.7 Å2
2---3.32 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→32.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6100 0 6 686 6792
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 626 5.1 %
Rwork0.263 11535 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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