[English] 日本語
Yorodumi- PDB-6hsp: Crystal structure of the zebrafish peroxisomal SCP2-thiolase (typ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hsp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1) in complex with CoA and octanoyl-CoA | ||||||
Components | SCP2-thiolase (type-1) | ||||||
Keywords | TRANSFERASE / thiolase fold / peroxisome / CoA binding | ||||||
Function / homology | Function and homology information alpha-linolenic acid (ALA) metabolism / Beta-oxidation of pristanoyl-CoA / 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 ...alpha-linolenic acid (ALA) metabolism / Beta-oxidation of pristanoyl-CoA / 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 / peroxisome / lipid binding / mitochondrion Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6hsp.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6hsp.ent.gz | 130 KB | Display | PDB format |
PDBx/mmJSON format | 6hsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hsp_validation.pdf.gz | 786.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6hsp_full_validation.pdf.gz | 790.4 KB | Display | |
Data in XML | 6hsp_validation.xml.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/6hsp ftp://data.pdbj.org/pub/pdb/validation_reports/hs/6hsp | HTTPS FTP |
-Related structure data
Related structure data | 6hrvSC 6hsjC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45105.281 Da / Num. of mol.: 2 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 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CO8 / | #4: Chemical | ChemComp-COA / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47.2 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM MOPS, pH 7.0, 10 % PEG6000, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.2822 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2822 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→42.88 Å / Num. obs: 85694 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.06 / Rsym value: 0.09 / Net I/σ(I): 8.42 |
Reflection shell | Resolution: 1.73→1.83 Å / Redundancy: 2.6 % / Num. unique obs: 12971 / CC1/2: 0.403 / Rpim(I) all: 0.38 / Rsym value: 0.63 / % possible all: 97.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HRV Resolution: 1.73→42.88 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.979 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.337 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.73→42.88 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.73→1.775 Å / Total num. of bins used: 20
|