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Yorodumi- PDB-1zmd: Crystal Structure of Human dihydrolipoamide dehydrogenase complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zmd | ||||||
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Title | Crystal Structure of Human dihydrolipoamide dehydrogenase complexed to NADH | ||||||
Components | Dihydrolipoyl dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / E3 / lipoamide dehydrogenase / pyruvate dehydrogenase / alpha-ketoglutarate dehydrogenase / branched-chain alpha-ketoacid dehydrogenase / glycine decarboxylase / glycine cleavage | ||||||
Function / homology | Function and homology information acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / Glycine degradation / PDH complex synthesizes acetyl-CoA from PYR / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / acetyl-CoA biosynthetic process from pyruvate / Lysine catabolism / Regulation of pyruvate dehydrogenase (PDH) complex ...acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / Glycine degradation / PDH complex synthesizes acetyl-CoA from PYR / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / acetyl-CoA biosynthetic process from pyruvate / Lysine catabolism / Regulation of pyruvate dehydrogenase (PDH) complex / branched-chain amino acid catabolic process / oxoglutarate dehydrogenase complex / pyruvate dehydrogenase complex / Branched-chain amino acid catabolism / motile cilium / sperm capacitation / Signaling by Retinoic Acid / gastrulation / regulation of membrane potential / mitochondrial electron transport, NADH to ubiquinone / Mitochondrial protein degradation / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / proteolysis / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Brautigam, C.A. / Chuang, J.L. / Tomchick, D.R. / Machius, M. / Chuang, D.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structure of Human Dihydrolipoamide Dehydrogenase: NAD+/NADH Binding and the Structural Basis of Disease-causing Mutations Authors: Brautigam, C.A. / Chuang, J.L. / Tomchick, D.R. / Machius, M. / 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 | 1zmd.cif.gz | 759.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zmd.ent.gz | 626.4 KB | Display | PDB format |
PDBx/mmJSON format | 1zmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zmd_validation.pdf.gz | 4.4 MB | Display | wwPDB validaton report |
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Full document | 1zmd_full_validation.pdf.gz | 4.5 MB | Display | |
Data in XML | 1zmd_validation.xml.gz | 156.3 KB | Display | |
Data in CIF | 1zmd_validation.cif.gz | 217.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/1zmd ftp://data.pdbj.org/pub/pdb/validation_reports/zm/1zmd | HTTPS FTP |
-Related structure data
Related structure data | 1zmcC 1jehS 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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Unit cell |
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-Components
#1: Protein | Mass: 50208.406 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLD, GCSL, LAD, PHE3 / Plasmid: PLASMID / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: P09622, dihydrolipoyl dehydrogenase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-FAD / #4: Chemical | ChemComp-NAI / #5: 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: 2.8 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: HEPES, PEG 4000, ammonium sulfate, pH 7.0, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97943 Å |
Detector | Type: APS / Detector: CCD / Date: Jul 10, 2004 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97943 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→33.1 Å / Num. all: 281138 / Num. obs: 281013 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.054 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.08→2.15 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 27865 / Rsym value: 0.434 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JEH Resolution: 2.08→33.06 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 5519904.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.2125 Å2 / ksol: 0.337679 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.08→33.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.21 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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