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Yorodumi- PDB-6hrv: Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hrv | ||||||
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Title | Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1) | ||||||
Components | (SCP2-thiolase (type-1)) x 2 | ||||||
Keywords | TRANSFERASE / Fatty acid metabolism / bile acid biosynthesis / peroxisomal beta-oxidation / thiolytic cleavage | ||||||
Function / homology | Function and homology information alpha-linolenic acid (ALA) metabolism / Beta-oxidation of pristanoyl-CoA / Peroxisomal protein import / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / propanoyl-CoA C-acyltransferase activity / propionyl-CoA C2-trimethyltridecanoyltransferase activity / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase ...alpha-linolenic acid (ALA) metabolism / Beta-oxidation of pristanoyl-CoA / Peroxisomal protein import / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / propanoyl-CoA C-acyltransferase activity / propionyl-CoA C2-trimethyltridecanoyltransferase activity / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / intracellular cholesterol transport / phospholipid transport / lipid metabolic process / peroxisome / lipid binding / mitochondrion Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Wierenga, R.K. / Kiema, T.R. / Thapa, C.J. | ||||||
Citation | Journal: Biochem. J. / Year: 2019 Title: The peroxisomal zebrafish SCP2-thiolase (type-1) is a weak transient dimer as revealed by crystal structures and native mass spectrometry. Authors: Kiema, T.R. / Thapa, C.J. / Laitaoja, M. / Schmitz, W. / Maksimainen, M.M. / Fukao, T. / Rouvinen, J. / Janis, J. / Wierenga, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hrv.cif.gz | 164 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hrv.ent.gz | 126.4 KB | Display | PDB format |
PDBx/mmJSON format | 6hrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/6hrv ftp://data.pdbj.org/pub/pdb/validation_reports/hr/6hrv | HTTPS FTP |
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-Related structure data
Related structure data | 6hsjC 6hspC 3zbgS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45805.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: scp2a, scp2 / Plasmid: pGS21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pGro7 References: UniProt: Q6P4V5, propanoyl-CoA C-acyltransferase |
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#2: Protein | Mass: 45821.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: scp2a, scp2 / Plasmid: pGS21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pGro7 References: UniProt: Q6P4V5, propanoyl-CoA C-acyltransferase |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 100 mM HEPES, pH 6.4, 18% PEG3350, 250 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→29.64 Å / Num. obs: 60799 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.03 / Rsym value: 0.05 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.94 / Num. unique obs: 8507 / CC1/2: 0.87 / Rpim(I) all: 0.22 / Rsym value: 0.42 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZBG Resolution: 1.95→29.64 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.693 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.134 / 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: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.182 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→29.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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