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Yorodumi- PDB-2iby: Crystallographic and kinetic studies of human mitochondrial aceto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iby | ||||||
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Title | Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase (T2): the importance of potassium and chloride for its structure and function | ||||||
Components | Acetyl-CoA acetyltransferase | ||||||
Keywords | TRANSFERASE / thiolase fold / potassium ion / chloride / beta-alpha-beta-alpha-beta-alpha-beta-beta topology / alpha-beta-alpha-beta-alpha layered structure | ||||||
Function / homology | Function and homology information C-acetyltransferase activity / metanephric proximal convoluted tubule development / ketone body metabolic process / propionyl-CoA biosynthetic process / Utilization of Ketone Bodies / Synthesis of Ketone Bodies / cholesterol O-acyltransferase activity / ketone body catabolic process / acetyl-CoA catabolic process / isoleucine catabolic process ...C-acetyltransferase activity / metanephric proximal convoluted tubule development / ketone body metabolic process / propionyl-CoA biosynthetic process / Utilization of Ketone Bodies / Synthesis of Ketone Bodies / cholesterol O-acyltransferase activity / ketone body catabolic process / acetyl-CoA catabolic process / isoleucine catabolic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / coenzyme A binding / acetyl-CoA biosynthetic process / Branched-chain amino acid catabolism / coenzyme A metabolic process / coenzyme A biosynthetic process / fatty acid beta-oxidation / response to starvation / potassium ion binding / Mitochondrial protein degradation / adipose tissue development / liver development / response to hormone / response to organic cyclic compound / mitochondrial matrix / enzyme binding / endoplasmic reticulum / mitochondrion / extracellular exosome / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Haapalainen, A.M. / Wierenga, R.K. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Crystallographic and Kinetic Studies of Human Mitochondrial Acetoacetyl-CoA Thiolase: The Importance of Potassium and Chloride Ions for Its Structure and Function Authors: Haapalainen, A.M. / Merilainen, G. / Pirila, P.L. / Kondo, N. / Fukao, T. / 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 | 2iby.cif.gz | 329 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iby.ent.gz | 265.1 KB | Display | PDB format |
PDBx/mmJSON format | 2iby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/2iby ftp://data.pdbj.org/pub/pdb/validation_reports/ib/2iby | HTTPS FTP |
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-Related structure data
Related structure data | 2ib7C 2ib8C 2ib9C 2ibuC 2ibwC 1wl4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit consists of one biological unit, the homotetramer |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41549.047 Da / Num. of mol.: 4 / Mutation: V34A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: liver / Gene: ACAT1 / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P24752, acetyl-CoA C-acetyltransferase |
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-Non-polymers , 6 types, 1177 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-COA / #5: Chemical | ChemComp-MES / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG 5000 monomethylether, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2006 / Details: mirrors |
Radiation | Monochromator: carved in a single Silicon (111) crystal whith a channel in the middle, called channel-cut design Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07225 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→73.32 Å / Num. all: 133490 / Num. obs: 133365 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 4.6 / Num. unique all: 19414 / Rsym value: 0.324 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1WL4 Resolution: 1.85→73.32 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.547 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.388 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→73.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.915 Å / Total num. of bins used: 15
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