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- PDB-5xpx: Structure elucidation of truncated AMS3 lipase from an Antarctic ... -

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Basic information

Entry
Database: PDB / ID: 5xpx
TitleStructure elucidation of truncated AMS3 lipase from an Antarctic Pseudomonas
ComponentsLipase
KeywordsHYDROLASE
Function / homologytriacylglycerol lipase / triacylglycerol lipase activity / Alpha/Beta hydrolase fold / extracellular region / metal ion binding / triacylglycerol lipase
Function and homology information
Biological speciesPseudomonas sp. A3
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsRahman, R.N.Z.R.A. / Latip, W.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Universiti Putra Malaysia9479200 Malaysia
CitationJournal: To Be Published
Title: Structure elucidation of truncated AMS3 lipase from an Antarctic Pseudomonas
Authors: Rahman, R.N.Z.R.A. / Latip, W.
History
DepositionJun 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
E: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1396
Polymers95,9282
Non-polymers2114
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-27 kcal/mol
Surface area28900 Å2
Unit cell
Length a, b, c (Å)86.753, 94.693, 126.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipase


Mass: 47964.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. A3(2015c) (bacteria) / Strain: 2015c
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0K0PTR1, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 0.8 M Potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: CCD / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.77→40 Å / Num. obs: 27263 / % possible obs: 99.7 % / Redundancy: 2.1 % / Net I/σ(I): 9.4
Reflection shellResolution: 2.77→2.82 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data processing
HKL-3000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FDM

4fdm


Resolution: 2.77→40 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.856 / SU B: 15.282 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2771 1391 5.2 %RANDOM
Rwork0.2217 ---
obs0.22463 25583 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.183 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å20 Å20 Å2
2---1.92 Å20 Å2
3----1.81 Å2
Refinement stepCycle: 1 / Resolution: 2.77→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 4 20 6066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196208
X-RAY DIFFRACTIONr_bond_other_d0.0020.025488
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9318440
X-RAY DIFFRACTIONr_angle_other_deg1.098312671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3065763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75123.013312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.32215942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9061551
X-RAY DIFFRACTIONr_chiral_restr0.0950.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217088
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021415
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6712.6793058
X-RAY DIFFRACTIONr_mcbond_other1.632.6773057
X-RAY DIFFRACTIONr_mcangle_it2.7664.0113819
X-RAY DIFFRACTIONr_mcangle_other2.7674.0123820
X-RAY DIFFRACTIONr_scbond_it1.5922.833150
X-RAY DIFFRACTIONr_scbond_other1.5922.8313151
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7044.1874622
X-RAY DIFFRACTIONr_long_range_B_refined4.5130.8357101
X-RAY DIFFRACTIONr_long_range_B_other4.5130.8367102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.767→2.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 92 -
Rwork0.318 1817 -
obs--96.41 %

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