+Open data
-Basic information
Entry | Database: PDB / ID: 3ab9 | ||||||
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Title | Crystal Structure of lipoylated E. coli H-protein (reduced form) | ||||||
Components | Glycine cleavage system H protein | ||||||
Keywords | TRANSPORT PROTEIN / glycine cleavage system / Lipoyl | ||||||
Function / homology | Function and homology information glycine cleavage complex / glycine decarboxylation via glycine cleavage system / one-carbon metabolic process / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Okamura-Ikeda, K. / Maita, N. | ||||||
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 | 3ab9.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ab9.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ab9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/3ab9 ftp://data.pdbj.org/pub/pdb/validation_reports/ab/3ab9 | HTTPS FTP |
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-Related structure data
Related structure data | 3a8iC 3a8jC 3a8kC 1hpcS 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: 14009.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. W3110 / Gene: gcvH / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A6T9 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-CL / |
#4: 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: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 95mM Hepes-Na, 0.19M CaCl2, 26.6% PEG400, 5% Glycerol, pH 7.5, 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: Mar 6, 2003 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→45 Å / Num. obs: 15779 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 79.8 |
Reflection shell | Resolution: 1.65→1.67 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 8.6 / Num. unique all: 555 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HPC Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.846 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.095 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.922 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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