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- PDB-1ex9: CRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LIPASE COMPLEXED ... -

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Basic information

Entry
Database: PDB / ID: 1ex9
TitleCRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LIPASE COMPLEXED WITH RC-(RP,SP)-1,2-DIOCTYLCARBAMOYL-GLYCERO-3-O-OCTYLPHOSPHONATE
ComponentsLACTONIZING LIPASE
KeywordsHYDROLASE / Lipase / alpha-beta hydrolase fold / Pseudomonas / phosphonate inhibitor
Function / homology
Function and homology information


lipase activity / protein transport by the Sec complex / protein secretion by the type II secretion system / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
Lipases, serine active site. / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-OCP / Triacylglycerol lipase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsNardini, M. / Lang, D.A. / Liebeton, K. / Jaeger, K.-E. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structure of pseudomonas aeruginosa lipase in the open conformation. The prototype for family I.1 of bacterial lipases.
Authors: Nardini, M. / Lang, D.A. / Liebeton, K. / Jaeger, K.E. / Dijkstra, B.W.
History
DepositionMay 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: 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 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LACTONIZING LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7793
Polymers30,1611
Non-polymers6192
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.470, 50.963, 110.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein LACTONIZING LIPASE / TRIACYL-GLYCEROL LIPASE


Mass: 30160.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PEL11 / Production host: Pseudomonas aeruginosa (bacteria) / Strain (production host): PAC1R / References: UniProt: P26876, triacylglycerol lipase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-OCP / OCTYL-PHOSPHINIC ACID 1,2-BIS-OCTYLCARBAMOYLOXY-ETHYL ESTER


Mass: 578.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H59N2O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: MPD, calcium chloride, citrate , pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mMTris-HCl1drop
31 %beta-octylpyranoside1drop
425 %MPD1reservoir
520 mM1reservoirCaCl2
6100 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 29, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→28.55 Å / Num. all: 34304 / Num. obs: 8772 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.119
Reflection shellResolution: 2.54→28.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.336 / Num. unique all: 1056 / % possible all: 98.2
Reflection
*PLUS
Num. measured all: 34304
Reflection shell
*PLUS
% possible obs: 98.2 % / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→28.55 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 413 -RANDOM
Rwork0.1951 ---
all0.1951 8739 --
obs0.1951 34304 98.3 %-
Refinement stepCycle: LAST / Resolution: 2.54→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 39 112 2276
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_bond_d0.012
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS

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