+Open data
-Basic information
Entry | Database: PDB / ID: 3a8j | ||||||
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Title | Crystal Structure of ET-EHred complex | ||||||
Components |
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Keywords | TRANSFERASE/TRANSPORT PROTEIN / Glycine Cleavage System / Aminotransferase / Transferase / Lipoyl / TRANSFERASE-TRANSPORT PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information aminomethyltransferase / aminomethyltransferase activity / glycine cleavage complex / glycine decarboxylation via glycine cleavage system / transaminase activity / one-carbon metabolic process / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Okamura-Ikeda, K. / Hosaka, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal structure of aminomethyltransferase in complex with dihydrolipoyl-H-protein of the glycine cleavage system: implications for recognition of lipoyl protein substrate, disease-related ...Title: Crystal structure of aminomethyltransferase in complex with dihydrolipoyl-H-protein of the glycine cleavage system: implications for recognition of lipoyl protein substrate, disease-related mutations, and reaction mechanism Authors: Okamura-Ikeda, K. / Hosaka, H. / Maita, N. / Fujiwara, K. / Yoshizawa, A.C. / Nakagawa, A. / Taniguchi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a8j.cif.gz | 358.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a8j.ent.gz | 292.1 KB | Display | PDB format |
PDBx/mmJSON format | 3a8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/3a8j ftp://data.pdbj.org/pub/pdb/validation_reports/a8/3a8j | HTTPS FTP |
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-Related structure data
Related structure data | 3a8iC 3a8kC 3ab9SC 1vloS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 40190.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 substr. W3110 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P27248, aminomethyltransferase #2: Protein | Mass: 14009.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 substr. W3110 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A6T9 #3: 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: 2.41 Å3/Da / Density % sol: 48.9 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 16% PEG8000, 0.04M KH2PO4, 20% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Dec 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 112820 / % possible obs: 98 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AB9 (EHred), 1VLO (ET) Resolution: 1.98→44.42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.156 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.822 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→44.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.982→2.033 Å / Total num. of bins used: 20
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