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- PDB-5lip: PSEUDOMONAS LIPASE COMPLEXED WITH RC-(RP, SP)-1,2-DIOCTYLCARBAMOY... -

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Basic information

Entry
Database: PDB / ID: 5lip
TitlePSEUDOMONAS LIPASE COMPLEXED WITH RC-(RP, SP)-1,2-DIOCTYLCARBAMOYLGLYCERO-3-O-OCTYLPHOSPHONATE
ComponentsTRIACYL-GLYCEROL HYDROLASE
KeywordsLIPASE / PSEUDOMONADACEAE / COVALENT INTERMEDIATE / TRIGLYCERIDE ANALOGUE / ENANTIOSELECTIVITY
Function / homology
Function and homology information


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 speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLang, D.A. / Dijkstra, B.W.
Citation
Journal: Eur.J.Biochem. / Year: 1998
Title: Structural basis of the chiral selectivity of Pseudomonas cepacia lipase
Authors: Lang, D.A. / Mannesse, M.L.M. / De Haas, G. / Verheij, H.M. / Dijkstra, B.W.
#1: Journal: Structure / Year: 1997
Title: The Open Conformation of a Pseudomonas Lipase
Authors: Schrag, J.D. / Li, Y. / Cygler, M. / Lang, D. / Burgdorf, T. / Hecht, H.J. / Schmid, R. / Schomburg, D. / Rydel, T.J. / Oliver, J.D. / Strickland, L.C. / Dunaway, C.M. / Larson, S.B. / Day, J. / McPherson, A.
#2: Journal: J.Bacteriol. / Year: 1991
Title: Extracellular Lipase of Pseudomonas Sp. Strain Atcc 21808: Purification, Characterization, Crystallization, and Preliminary X-Ray Diffraction Data
Authors: Kordel, M. / Hofmann, B. / Schomburg, D. / Schmid, R.D.
History
DepositionSep 2, 1997Processing site: BNL
Revision 1.0Aug 19, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIACYL-GLYCEROL HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7703
Polymers33,1511
Non-polymers6192
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.730, 46.420, 83.950
Angle α, β, γ (deg.)90.00, 121.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRIACYL-GLYCEROL HYDROLASE / LIPASE


Mass: 33150.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Cellular location: EXTRACELLULAR / Plasmid: PHES12 / Production host: Pseudomonas sp. (bacteria) / Strain (production host): 21808 / References: UniProt: P22088, 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.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE STARTING MATERIAL FOR THE INHIBITOR WAS RC-(RP,SP)-1,2- DIOCTYLCARBAMOYL-GLYCERO-3-O-P- ...THE STARTING MATERIAL FOR THE INHIBITOR WAS RC-(RP,SP)-1,2- DIOCTYLCARBAMOYL-GLYCERO-3-O-P-NITROPHENYL- OCTYLPHOSPHONATE. BY THE REACTION DESCRIBED IN THE JNRL ABOVE, THIS TURNED INTO RC-SP-1,2-DIOCTYLCARBAMOYL-GLYCERO-3-O-OCTYLPHOSPHONATE, COVALENTLY BOUND TO THE PROTEIN.

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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 %
Crystal growpH: 4
Details: 14 % ISOPROPANOL, 0.020 M CACL2, 0.1 M ACETATE, PH 4, pH 4.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 9 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
220 mMglycine1drop
314 %isopropanol1reservoir
420 mM1reservoirCaCl2
5100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 6515 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.092 / Net I/σ(I): 7.1
Reflection shellResolution: 2.9→2.95 Å / Rsym value: 0.158 / % possible all: 87.2
Reflection
*PLUS
Num. measured all: 22335 / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
Rmerge(I) obs: 0.158

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LIP

3lip


Resolution: 2.9→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 0
Details: THE CIS-PEPTIDE BOND VISIBLE IN THE HIGH RESOLUTION STRUCTURES COULD NOT BE KEPT AT 2.9 ANG.
RfactorNum. reflection% reflection
Rfree0.285 -9 %
Rwork0.206 --
obs0.206 6221 98.5 %
Displacement parametersBiso mean: 7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 39 4 2378
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.98
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.9→3.03 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.27 -
Rwork0.23 623
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2OCP.PROOCP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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