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- PDB-1cvl: CRYSTAL STRUCTURE OF BACTERIAL LIPASE FROM CHROMOBACTERIUM VISCOS... -

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Basic information

Entry
Database: PDB / ID: 1cvl
TitleCRYSTAL STRUCTURE OF BACTERIAL LIPASE FROM CHROMOBACTERIUM VISCOSUM ATCC 6918
ComponentsTRIACYLGLYCEROL HYDROLASE
KeywordsHYDROLASE / TRIACYLGLYCEROL-HYDROLASE / PSEUDOMONADACEAE / OXYANION / CIS-PEPTIDE
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 / Triacylglycerol lipase
Similarity search - Component
Biological speciesChromobacterium viscosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsLang, D.A. / Hofmann, B. / Haalck, L. / Hecht, H.-J. / Spener, F. / Schmid, R.D. / Schomburg, D.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of a bacterial lipase from Chromobacterium viscosum ATCC 6918 refined at 1.6 angstroms resolution.
Authors: Lang, D. / Hofmann, B. / Haalck, L. / Hecht, H.J. / Spener, F. / Schmid, R.D. / Schomburg, D.
History
DepositionJan 9, 1997Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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: TRIACYLGLYCEROL HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1582
Polymers33,1181
Non-polymers401
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.080, 156.820, 43.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TRIACYLGLYCEROL HYDROLASE


Mass: 33117.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CHAIN BREAK FROM V 220 - G 222 / Source: (natural) Chromobacterium viscosum (bacteria)
References: UniProt: Q05489, UniProt: P0DUB9*PLUS, 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.: 230 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPARTLY DEGRADED LIPASE AS A RESULT OF UNSPECIFIC PROTEOLYTIC DIGESTION DURING PURIFICATION AND/OR ...PARTLY DEGRADED LIPASE AS A RESULT OF UNSPECIFIC PROTEOLYTIC DIGESTION DURING PURIFICATION AND/OR STORAGE PROVEN BY MALDI-TOF MASS SPECTROSCOPY MOLECULAR WEIGHT: CALCULATED -- 33091 DALTON MEASURED -- 32839 DALTON LEU 17 AND THR 20 ARE RESIDUES LOCATED ON THE OXYANION LOOP, A STRUCTURAL MOTIF, WHICH IS IMPORTANT FOR THE STABILIZATION OF THE NEGATIVE CHARGE OF THE TETRAHEDRAL INTERMEDIATE DURING ENZYME CATALYSIS. THEY POSSESS AN ENERGETICALLY HIGHER CONFORMATION ACTIVE SITE SER 87 HAS THE TYPICAL CONFORMATION FOR THE NUCLEOPHILE OF A ALPHA/BETA HYDROLASE FOLD ENZYME.
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: 2.15 Å3/Da / Density % sol: 42 %
Crystal growpH: 6.4
Details: PROTEIN WAS CRYSTALLIZED FROM 10-14 % PEG 4000, 10-14 % MPD, 100 MM CITRATE/PHOSPHATE BUFFER, PH 6.4
Crystal grow
*PLUS
Temperature: 292 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mllipase1drop
25 mMTris-HCl1drop
30.25 %(w/v)n-octyl-beta-D-glycopyranoside1drop
414 %(w/v)PEG40001reservoir
510-14 %(v/v)MPD1reservoir
6100 mMcitrate-phosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 33644 / % possible obs: 88 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 8.5
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.053 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.22 / % possible all: 73.7
Reflection
*PLUS
Num. measured all: 87722
Reflection shell
*PLUS
% possible obs: 73.7 % / Rmerge(I) obs: 0.22

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Processing

Software
NameClassification
MOSFLMdata reduction
CCP4data reduction
MLPHAREphasing
PROLSQrefinement
CCP4data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.6→8 Å / Cross valid method: RANDOM / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.178 --
all-32395 -
obs-32395 88 %
Displacement parametersBiso mean: 14.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 1 230 2547
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0440.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.31
X-RAY DIFFRACTIONp_mcangle_it2.051.5
X-RAY DIFFRACTIONp_scbond_it1.641
X-RAY DIFFRACTIONp_scangle_it2.261.5
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.0820.075
X-RAY DIFFRACTIONp_singtor_nbd0.1690.3
X-RAY DIFFRACTIONp_multtor_nbd0.2120.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.7043
X-RAY DIFFRACTIONp_staggered_tor13.0715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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