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Yorodumi- PDB-1cvl: CRYSTAL STRUCTURE OF BACTERIAL LIPASE FROM CHROMOBACTERIUM VISCOS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cvl | ||||||
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Title | CRYSTAL STRUCTURE OF BACTERIAL LIPASE FROM CHROMOBACTERIUM VISCOSUM ATCC 6918 | ||||||
Components | TRIACYLGLYCEROL HYDROLASE | ||||||
Keywords | HYDROLASE / 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 | ||||||
Biological species | Chromobacterium viscosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å | ||||||
Authors | Lang, D.A. / Hofmann, B. / Haalck, L. / Hecht, H.-J. / Spener, F. / Schmid, R.D. / Schomburg, D. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cvl.cif.gz | 68 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cvl.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 1cvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cvl_validation.pdf.gz | 414.3 KB | Display | wwPDB validaton report |
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Full document | 1cvl_full_validation.pdf.gz | 421.3 KB | Display | |
Data in XML | 1cvl_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1cvl_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/1cvl ftp://data.pdbj.org/pub/pdb/validation_reports/cv/1cvl | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Compound details | PARTLY DEGRADED LIPASE AS A RESULT OF UNSPECIFIC PROTEOLYTIC DIGESTION DURING PURIFICATION AND/OR ...PARTLY DEGRADED LIPASE AS A RESULT OF UNSPECIFIC |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.6→8 Å / Cross valid method: RANDOM / σ(F): 0
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Displacement parameters | Biso mean: 14.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |