+Open data
-Basic information
Entry | Database: PDB / ID: 2w7j | ||||||
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Title | Crystal structure of Y61AbsSHMT Glycine external aldimine | ||||||
Components | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ONE-CARBON METABOLISM / PLP-DEPENDENT ENZYMES | ||||||
Function / homology | Function and homology information serine binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | GEOBACILLUS STEAROTHERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Rajaram, V. / Bhavani, B.S. / Bisht, S. / Kaul, P. / Prakash, V. / Appaji Rao, N. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Citation | Journal: FEBS J. / Year: 2008 Title: Importance of Tyrosine Residues of Bacillus Stearothermophilus Serine Hydroxymethyltransferase in Cofactor Binding and L-Allo-Thr Cleavage. Authors: Bhavani, B.S. / Rajaram, V. / Bisht, S. / Kaul, P. / Prakash, V. / Murthy, M.R.N. / Appaji Rao, N. / Savithri, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w7j.cif.gz | 100 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w7j.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 2w7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/2w7j ftp://data.pdbj.org/pub/pdb/validation_reports/w7/2w7j | HTTPS FTP |
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-Related structure data
Related structure data | 2w7dC 2w7eC 2w7fC 2w7gC 2w7hC 2w7iC 2w7kC 2w7lC 2w7mC 1kl1S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44182.086 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-405 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q7SIB6, glycine hydroxymethyltransferase |
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#2: Chemical | ChemComp-GLY / |
#3: Chemical | ChemComp-PLP / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | Details: 50% MPD, 0.1 M HEPES PH7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM GLYCINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→30 Å / Num. obs: 42717 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.66→1.72 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.2 / % possible all: 89.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KL1 Resolution: 1.68→22.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.047 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.107 / 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: 17.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→22.24 Å
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Refine LS restraints |
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