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- PDB-3lip: OPEN CONFORMATION OF PSEUDOMONAS CEPACIA LIPASE -

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Open data


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Basic information

Entry
Database: PDB / ID: 3lip
TitleOPEN CONFORMATION OF PSEUDOMONAS CEPACIA LIPASE
ComponentsTRIACYL-GLYCEROL-HYDROLASE
KeywordsHYDROLASE / LIPASE / PSEUDOMONADACEAE / CATALYTIC TRIAD / OXYANION / OPEN / WITHOUT INHIBITOR
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
Triacylglycerol lipase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLang, D.A. / Schomburg, D.
Citation
#1: Journal: Biochim.Biophys.Acta / Year: 1994
Title: Lipase of Pseudomonas Cepacia for Biotechnological Purposes: Purification, Crystallization and Characterization
Authors: Bornscheuer, U. / Reif, O.W. / Lausch, R. / Freitag, R. / Scheper, T. / Kolisis, F.N. / Menge, U.
#2: Journal: To Be Published / Year: 1994
Title: Structure Elucidation of Two Lipases of the Pseudomonas Family
Authors: Lang, D.A. / Hofmann, B. / Burgdorf, T. / Haalck, L. / Hecht, H.-J. / Spener, F. / Schmid, R.D. / Schomburg, D.
History
DepositionApr 18, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: 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: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)33,1912
Polymers33,1511
Non-polymers401
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.300, 47.300, 85.400
Angle α, β, γ (deg.)90.00, 121.40, 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 natural source / Source: (natural) Burkholderia cepacia (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 285 K / pH: 8.7
Details: 29-30 % N-PROPANOL, 0.1 M TRIS HCL BUFFER, PH 8.4-8.7, AT 12 DEGREES IN FOUR WEEKS, PROTEIN CONCENTRATION 22 MG/ML, temperature 285K
PH range: 8.4-8.7
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
129-30 %(v/v)1-propanol1reservoir
2100 mMTris-HCl1reservoirpH8.5-8.7
322 mg/mlprotein1drop
410 mMTris-HCl1droppH7.5

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1994 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→18.7 Å / Num. obs: 17688 / % possible obs: 83.3 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 0.095
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.63 % / Rsym value: 0.183 / % possible all: 83.1
Reflection
*PLUS
Num. measured all: 33550 / Rmerge(I) obs: 0.095

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PROLSQrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CVL

1cvl


Resolution: 2→8 Å / σ(F): 0
Details: DENSITY FOR RESIDUES 217 - 223 IS FRAGMENTED. THEREFORE THIS REGION WAS MODELED STEREOCHEMICALLY. THE ELECTRON DENSITY FOR THE RESIDUES THR 18, SER 87, THR 217 AND LEU 234 IS WELL DEFINED IN ...Details: DENSITY FOR RESIDUES 217 - 223 IS FRAGMENTED. THEREFORE THIS REGION WAS MODELED STEREOCHEMICALLY. THE ELECTRON DENSITY FOR THE RESIDUES THR 18, SER 87, THR 217 AND LEU 234 IS WELL DEFINED IN SPITE OF DIHEDRAL ANGLES OF THESE RESIDUES LYING OUTSIDE THEIR EXPECTED RANGE.
RfactorNum. reflection% reflection
Rwork0.188 --
all-17424 -
obs-17424 83 %
Displacement parametersBiso mean: 12.95 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 1 193 2532
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0520.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.05
X-RAY DIFFRACTIONp_mcbond_it1.5121
X-RAY DIFFRACTIONp_mcangle_it2.4061.5
X-RAY DIFFRACTIONp_scbond_it1.4741
X-RAY DIFFRACTIONp_scangle_it2.021.5
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.0860.08
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.1380.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.3
X-RAY DIFFRACTIONp_planar_tor2.3873
X-RAY DIFFRACTIONp_staggered_tor12.03115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.91915
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor all: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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