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- PDB-2fx5: Pseudomonas mendocina lipase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2fx5
TitlePseudomonas mendocina lipase
Componentslipase
KeywordsHYDROLASE / alpha-beta hydrolase
Function / homology
Function and homology information


Cutinase / PET hydrolase-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / PET hydrolase/cutinase-like domain-containing protein / PET hydrolase/cutinase-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsBott, R. / Wu, S.
History
DepositionFeb 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THERE WAS NO SEQUENCE DATABASE REFERENCE AT TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7792
Polymers27,6291
Non-polymers1501
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.50, 58.50, 145.00
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

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Components

#1: Protein lipase


Mass: 27628.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Production host: Bacillus subtilis (bacteria)
References: UniProt: Q9HXQ8, UniProt: A4Y035*PLUS, triacylglycerol lipase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50 mM sodium acetate, 18% saturated potassium tartrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1991
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 19100 / % possible obs: 95 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
PROTEINmodel building
PROLSQrefinement
PROTEINphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→10 Å / σ(F): 2 /
RfactorNum. reflection
all0.178 19100
obs-19100
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 10 104 2061
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d3.1
X-RAY DIFFRACTIONp_planar_d0.02

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