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Open data
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Basic information
Entry | Database: PDB / ID: 3a8i | ||||||
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Title | Crystal Structure of ET-EHred-5-CH3-THF complex | ||||||
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![]() | TRANSFERASE/TRANSPORT PROTEIN / Glycine Cleavage System / Aminotransferase / Transferase / Lipoyl / TRANSFERASE-TRANSPORT PROTEIN COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okamura-Ikeda, K. / Hosaka, H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 359.2 KB | Display | ![]() |
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PDB format | ![]() | 292.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3a8jSC ![]() 3a8kC ![]() 3ab9C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 14009.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-C2F / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.43 % |
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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: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Apr 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→30 Å / Num. obs: 97181 / % possible obs: 85.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.78 |
Reflection shell | Resolution: 1.99→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A8J Resolution: 1.99→29.77 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.365 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.203 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.557 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→29.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.994→2.046 Å / Total num. of bins used: 20
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