+Open data
-Basic information
Entry | Database: PDB / ID: 2vgt | ||||||
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Title | Crystal structure of E53QbsSHMT with glycine | ||||||
Components | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / PLP-DEPENDENT ENZYMES / 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: 1.86 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 | 2vgt.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vgt.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vgt_validation.pdf.gz | 430.9 KB | Display | wwPDB validaton report |
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Full document | 2vgt_full_validation.pdf.gz | 431.8 KB | Display | |
Data in XML | 2vgt_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 2vgt_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/2vgt ftp://data.pdbj.org/pub/pdb/validation_reports/vg/2vgt | HTTPS FTP |
-Related structure data
Related structure data | 2vgsC 2vguC 2vgvC 2vgwC 1kl1S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44387.301 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-405 / Mutation: YES Source method: isolated from a genetically manipulated source 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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-Non-polymers , 5 types, 445 molecules
#2: Chemical | ChemComp-GLY / |
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#3: Chemical | ChemComp-PLP / |
#4: Chemical | ChemComp-MPD / ( |
#5: Chemical | ChemComp-PO4 / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEERED |
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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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 50 % MPD, 0.1 M HEPES, 0.2 MM EDTA, 5 MM 2-MECAPTOETHANOL, 10 MM GLYCINE, pH 7.5 |
-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: 1.86→50 Å / Num. obs: 304348 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1KL1 Resolution: 1.86→28.65 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.67 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.141 / 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: 18.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→28.65 Å
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Refine LS restraints |
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