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Yorodumi- PDB-2f60: Crystal Structure of the Dihydrolipoamide Dehydrogenase (E3)-Bind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f60 | ||||||
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Title | Crystal Structure of the Dihydrolipoamide Dehydrogenase (E3)-Binding Domain of Human E3-Binding Protein | ||||||
Components | Pyruvate dehydrogenase protein X component | ||||||
Keywords | PROTEIN BINDING / protein-binding protein / E3BD | ||||||
Function / homology | Function and homology information acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / : / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / acyltransferase activity / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Brautigam, C.A. / Chuang, J.L. / Wynn, R.M. / Tomchick, D.R. / Machius, M. / Chuang, D.T. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Structural Insight into Interactions between Dihydrolipoamide Dehydrogenase (E3) and E3 Binding Protein of Human Pyruvate Dehydrogenase Complex. Authors: Brautigam, C.A. / Wynn, R.M. / Chuang, J.L. / Machius, M. / Tomchick, D.R. / Chuang, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f60.cif.gz | 26.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f60.ent.gz | 16.9 KB | Display | PDB format |
PDBx/mmJSON format | 2f60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/2f60 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/2f60 | HTTPS FTP |
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-Related structure data
Related structure data | 2f5zSC 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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Unit cell |
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-Components
#1: Protein | Mass: 7150.151 Da / Num. of mol.: 1 / Fragment: E3-binding domain, residues 173-230 / Mutation: K120G, T176L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDHX, PDX1 / Plasmid: pET-LTE3BD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O00330 | ||
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#2: Chemical | #3: 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: 2.62 Å3/Da / Density % sol: 53.11 % |
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Crystal grow | Temperature: 293 K / pH: 6.3 Details: 1.35 M sodium citrate, 0.075% beta-octyl-glucopyranoside, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.30 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2004 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→28.5 Å / Num. obs: 12109 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.032 / Net I/σ(I): 67.8 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 8.6 / Rsym value: 0.148 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2F5Z Resolution: 1.55→28.5 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 26 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→28.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.026
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