+Open data
-Basic information
Entry | Database: PDB / ID: 2vgs | ||||||
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Title | Crystal structure of E53QbsSHMT internal aldimine | ||||||
Components | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / PLP-DEPENDENT ENZYMES / SERINE HYDROXYMETHYLTRANSFERASE / SHMT / E53Q / ENZYME MEMORY / PYRIDOXAL PHOSPHATE / ONE-CARBON METABOLISM | ||||||
Function / homology | Function and homology information glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / 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 | BACILLUS STEAROTHERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Rajaram, V. / Bhavani, B.S. / Kaul, P. / Prakash, V. / Appaji Rao, N. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Citation | Journal: FEBS J. / Year: 2007 Title: Structure Determination and Biochemical Studies on Bacillus Stearothermophilus E53Q Serine Hydroxymethyltransferase and its Complexes Provide Insights on Function and Enzyme Memory Authors: Rajaram, V. / Bhavani, B.S. / Kaul, P. / Prakash, V. / Appaji Rao, N. / Savithri, H.S. / Murthy, M.R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vgs.cif.gz | 95.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vgs.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vgs_validation.pdf.gz | 406.9 KB | Display | wwPDB validaton report |
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Full document | 2vgs_full_validation.pdf.gz | 407.6 KB | Display | |
Data in XML | 2vgs_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 2vgs_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/2vgs ftp://data.pdbj.org/pub/pdb/validation_reports/vg/2vgs | HTTPS FTP |
-Related structure data
Related structure data | 2vgtC 2vguC 2vgvC 2vgwC 1kkjS 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: 44387.301 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-405 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SCHIFF LINKAGE BETWEEN LYS A 226 AND PLP B 501 / Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q7SIB6, glycine hydroxymethyltransferase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-MPD / ( |
#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 | pH: 7.5 Details: 50% MPD, 0.1 M HEPES PH 7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL |
-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 MIRROR |
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: 2→50 Å / Num. obs: 25550 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.7 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1KKJ Resolution: 2→29.36 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.926 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.174 / 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: 22.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.36 Å
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Refine LS restraints |
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