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- PDB-4lip: PSEUDOMONAS LIPASE COMPLEXED WITH RC-(RP, SP)-DIBUTYLCARBAMOYLGLY... -

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Basic information

Entry
Database: PDB / ID: 4lip
TitlePSEUDOMONAS LIPASE COMPLEXED WITH RC-(RP, SP)-DIBUTYLCARBAMOYLGLYCERO-3-O-BUTYLPHOSPHONATE
ComponentsTRIACYL-GLYCEROL-HYDROLASE
KeywordsLIPASE / HYDROLASE / 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
BUTYLPHOSPHONATE / Triacylglycerol lipase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
DepositionAug 18, 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: 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: TRIACYL-GLYCEROL-HYDROLASE
E: TRIACYL-GLYCEROL-HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6586
Polymers66,3022
Non-polymers3564
Water10,142563
1
D: TRIACYL-GLYCEROL-HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3293
Polymers33,1511
Non-polymers1782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: TRIACYL-GLYCEROL-HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3293
Polymers33,1511
Non-polymers1782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.040, 46.360, 85.380
Angle α, β, γ (deg.)90.00, 116.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9998, 0.0208, 0.001), (0.0208, 0.9996, -0.0187), (-0.0014, -0.0187, -0.9998)
Vector: 22.931, 0.441, 38.111)

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Components

#1: Protein TRIACYL-GLYCEROL-HYDROLASE / LIPASE


Mass: 33150.766 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CCP / BUTYLPHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H11O3P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STARTING MATERIAL FOR THE INHIBITOR WAS RC-(RP,SP)-1,2-DIBUTYLCARBAMOYL-GLYCERO-3-O-P- ...THE STARTING MATERIAL FOR THE INHIBITOR WAS RC-(RP,SP)-1,2-DIBUTYLCARBAMOYL-GLYCERO-3-O-P-NITROPHENYL BUTYLPHOSPHONATE. BY THE REACTION DESCRIBED IN THE JRNL REFERENCE ABOVE, THIS WAS TURNED INTO RC-SP-1,2-DIBUTYLCARBAMOYL-GLYCERO-3-O-BUTYLPHOSPHONATE. THE INHIBITOR IS COVALENTLY BOUND TO THE PROTEIN, BUT ONLY THE BUTYL PHOSPHONATE (SN-3 MOIETY) IS VISIBLE IN THE ELECTRON DENSITY. THIS IS NOT CAUSED BY FLEXIBILITY OR DISORDER, BUT THE PHOSPHONATE ESTER HAS BEEN CLEAVED BY AN AGING REACTION (BENCSURA ET AL. (1995), BIOCHEM. 34, 8989).

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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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growpH: 8.5 / Details: 20 % MPD, 100 MM CACL2, 0.1 M TRIS/HCL, PH 8.5
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
320 %MPD1reservoir
4100 mM1reservoirCaCl2
5100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 56937 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2.46 % / Rsym value: 0.031 / Net I/σ(I): 45.8
Reflection shellResolution: 1.75→1.83 Å / Mean I/σ(I) obs: 26.2 / Rsym value: 0.059 / % possible all: 93.9
Reflection
*PLUS
Num. measured all: 140279 / Rmerge(I) obs: 0.031
Reflection shell
*PLUS
Rmerge(I) obs: 0.059

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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: 1.75→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 0
Details: THE STRUCTURE WAS INITIALLY REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY, AND THEN WITH TIGHTLY RESTRAINED NON-CRYSTALLOGRAPHIC SYMMETRY FOR ALL PARTS OF THE MOLECULE EXCEPT RESIDUES 16 ...Details: THE STRUCTURE WAS INITIALLY REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY, AND THEN WITH TIGHTLY RESTRAINED NON-CRYSTALLOGRAPHIC SYMMETRY FOR ALL PARTS OF THE MOLECULE EXCEPT RESIDUES 16 - 28, 127 - 159, AND 218 - 224. THE CHAINS ARE NAMED D AND E, WITH MOLECULE D AS THE REFERENCE FOR SECONDARY STRUCTURE DEFINITION. DEVIATIONS FROM NON-CRYSTALLOGRAPHIC SYMMETRY CORRESPOND TO THOSE PARTS OF THE PROTEIN EXCLUDED FROM THE NCS-RESTRAINT.
RfactorNum. reflection% reflection
Rfree0.202 -3 %
Rwork0.178 --
obs0.178 56677 95.3 %
Displacement parametersBiso mean: 8.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 16 563 5237
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1
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
Refine LS restraints NCSNCS model details: PARTIAL RESTRAINT
LS refinement shellResolution: 1.75→1.83 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.232 -
Rwork0.22 6644
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2CCP.PROCCP.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_deg21.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1

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