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Yorodumi- PDB-2y6v: Peroxisomal alpha-beta-hydrolase Lpx1 (Yor084w) from Saccharomyce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y6v | ||||||
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Title | Peroxisomal alpha-beta-hydrolase Lpx1 (Yor084w) from Saccharomyces cerevisiae (crystal form I) | ||||||
Components | PEROXISOMAL MEMBRANE PROTEIN LPX1 | ||||||
Keywords | HYDROLASE / PUTATIVE ESTERASE / PUTATIVE LIPASE | ||||||
Function / homology | Function and homology information triglyceride catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / triglyceride lipase activity / peroxisomal matrix Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | ||||||
Authors | Thoms, S. / Niemann, H.H. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: The Unusual Extended C-Terminal Helix of the Peroxisomal Alpha-Beta-Hydrolase Lpx1 is Involved in Dimer Contacts But Dispensable for Dimerization Authors: Thoms, S. / Hofhuis, J. / Thoing, C. / Gartner, J. / Niemann, H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y6v.cif.gz | 439.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y6v.ent.gz | 379.1 KB | Display | PDB format |
PDBx/mmJSON format | 2y6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/2y6v ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y6v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 45208.359 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PST281 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS RIL References: UniProt: Q12405, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | C-TERMINAL ELEVEN RESIDUES ARE CLONING ARTEFACT (AAALE) AND HEXA-HISTIDINE TAG. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: HANGING OR SITTING DROP VAPOR DIFFUSION AT 20 DEGREES CELSIUS. 4 UL OF PROTEIN (7.9 MG/ML) MIXED WITH 2UL RESERVOIR (0.1 M HEPES, PH 7.5, 10 % PEG 8000). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Sep 3, 2008 / Details: VARIMAX HF CONFOCAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→20 Å / Num. obs: 34876 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.83→2.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.97 / % possible all: 68.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ENSEMBLE OF TEN ALPHA-BETA HYDROLASES AS POLY-ALA MODELS TRIMMED TO THE COMMON CORE. Resolution: 2.83→19.75 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.875 / SU B: 30.988 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.557 Å2
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Refinement step | Cycle: LAST / Resolution: 2.83→19.75 Å
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Refine LS restraints |
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