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- PDB-8yzn: Crystal structural analysis of PaL -

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Basic information

Entry
Database: PDB / ID: 8yzn
TitleCrystal structural analysis of PaL
ComponentsLipase
KeywordsBIOSYNTHETIC PROTEIN / Lipase / Pseudomonas alcaligenes / L-menthol
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / dipeptidyl-peptidase activity
Similarity search - Function
Xaa-Pro dipeptidyl-peptidase, C-terminal / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / : / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesPseudomonas alcaligenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.799 Å
AuthorsXu, G. / Wu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Structure / Year: 2024
Title: Crystal structure of lipase from Pseudomonas aeruginosa reveals an unusual catalytic triad conformation.
Authors: Xu, G. / Guo, H. / Yu, Z. / Wang, S. / Shen, D. / Yang, L. / Wu, J. / Chen, B. / Yu, H.
History
DepositionApr 7, 2024Deposition site: PDBJ / Processing site: PDBC
SupersessionApr 17, 2024ID: 8JJ7
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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: Lipase


Theoretical massNumber of molelcules
Total (without water)52,8211
Polymers52,8211
Non-polymers00
Water9,944552
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.774, 104.782, 62.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-750-

HOH

21A-952-

HOH

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Components

#1: Protein Lipase


Mass: 52821.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas alcaligenes (bacteria) / Gene: lip / Production host: Escherichia coli (E. coli) / References: UniProt: H9MZI2, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.29 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Disodium malonate 0.1 M, pH7.0 , PEG3350 18%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.799→24.164 Å / Num. obs: 48967 / % possible obs: 96.99 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.8
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 49315

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.799→24.164 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.087 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.098
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1757 1999 4.082 %
Rwork0.1445 46968 -
all0.146 --
obs-48967 96.928 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.238 Å2
Baniso -1Baniso -2Baniso -3
1--2.711 Å2-0 Å2-0 Å2
2--1.125 Å2-0 Å2
3---1.586 Å2
Refinement stepCycle: LAST / Resolution: 1.799→24.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 0 552 4284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0113835
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163604
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6335251
X-RAY DIFFRACTIONr_angle_other_deg0.5191.568273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.453523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54510549
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.39710150
X-RAY DIFFRACTIONr_chiral_restr0.0760.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024615
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02881
X-RAY DIFFRACTIONr_nbd_refined0.2180.2693
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23224
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21888
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2413
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.140.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.28
X-RAY DIFFRACTIONr_nbd_other0.2180.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.237
X-RAY DIFFRACTIONr_mcbond_it2.2441.8572026
X-RAY DIFFRACTIONr_mcbond_other2.2441.8572026
X-RAY DIFFRACTIONr_mcangle_it3.4263.3282533
X-RAY DIFFRACTIONr_mcangle_other3.4263.3282534
X-RAY DIFFRACTIONr_scbond_it3.1592.1171809
X-RAY DIFFRACTIONr_scbond_other3.1582.1171810
X-RAY DIFFRACTIONr_scangle_it4.6963.7292717
X-RAY DIFFRACTIONr_scangle_other4.6953.7292718
X-RAY DIFFRACTIONr_lrange_it6.60321.2834463
X-RAY DIFFRACTIONr_lrange_other6.43719.0784273
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.799-1.8450.231400.20133050.20236740.9630.97393.7670.182
1.845-1.8960.1761410.16633220.16735590.9790.98197.30260.143
1.896-1.950.2291390.16332620.16634860.9660.98197.56170.14
1.95-2.010.1621350.1431870.1433910.9820.98797.96520.122
2.01-2.0750.1911310.14430560.14632580.9750.98697.82070.126
2.075-2.1470.1891290.14630260.14732240.980.98797.85980.129
2.147-2.2280.1871190.13628150.13830510.9780.98896.16520.12
2.228-2.3180.1591190.13527870.13629550.9840.98898.34180.121
2.318-2.420.1771130.13126580.13328290.980.98997.94980.119
2.42-2.5370.1991100.13125790.13427340.9780.98998.35410.12
2.537-2.6720.1691040.13324450.13425830.9820.98998.68370.124
2.672-2.8320.215970.14722670.14924980.9740.98694.63570.139
2.832-3.0250.18920.13921730.14123100.9820.98898.05190.135
3.025-3.2630.16880.14520650.14521860.9820.98798.49040.145
3.263-3.5680.184820.15718960.15820120.9830.98698.31010.16
3.568-3.9780.169730.14817210.14918320.9820.98797.92580.156
3.978-4.5730.142630.12214830.12316430.990.99194.09620.133
4.573-5.5520.138550.13113150.13114070.9930.99297.37030.144
5.552-7.6520.186440.17610210.17711280.9840.98494.41490.194
7.652-24.1640.127250.1545850.1537260.9880.98684.0220.173

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