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Yorodumi- PDB-2vgv: Crystal structure of E53QbsSHMT obtained in the presence of L-all... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vgv | ||||||
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Title | Crystal structure of E53QbsSHMT obtained in the presence of L-allo- Threonine | ||||||
Components | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / PLP-DEPENDENT ENZYMES / SHMT / E53Q / ENZYME MEMORY / PYRIDOXAL PHOSPHATE / ONE-CARBON METABOLISM | ||||||
Function / homology | Function and homology information serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / 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: 2.3 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 | 2vgv.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vgv.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vgv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/2vgv ftp://data.pdbj.org/pub/pdb/validation_reports/vg/2vgv | HTTPS FTP |
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-Related structure data
Related structure data | 2vgsC 2vgtC 2vguC 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
#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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#2: Chemical | ChemComp-GLY / |
#3: Chemical | ChemComp-PLP / |
#4: Chemical | ChemComp-MPD / ( |
#5: 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, 10 MM L-ALLO-THREONINE |
-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: 2.3→50 Å / Num. obs: 16978 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.7 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1KL1 Resolution: 2.3→29.37 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.858 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.765 / ESU R Free: 0.276 / 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: 25.16 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.37 Å
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Refine LS restraints |
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