+Open data
-Basic information
Entry | Database: PDB / ID: 2vmv | ||||||
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Title | Crystal structure of F351GbsSHMT internal aldimine | ||||||
Components | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / PLP-DEPENDENT ENZYMES / F351G / FOLATE BINDING / 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: 1.7 Å | ||||||
Authors | Rajaram, V. / Pai, V.R. / Bisht, S. / Bhavani, B.S. / Appaji Rao, N. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Citation | Journal: Biochem.J. / Year: 2009 Title: Structural and Functional Studies of Bacillus Stearothermophilus Serine Hydroxymethyltransferase: The Role of Asn(341), Tyr(60) and Phe(351) in Tetrahydrofolate Binding. Authors: Pai, V.R. / Rajaram, V. / Bisht, S. / Bhavani, B.S. / Rao, N.A. / Murthy, M.R.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 | 2vmv.cif.gz | 98.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vmv.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 2vmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vmv_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 2vmv_full_validation.pdf.gz | 455.8 KB | Display | |
Data in XML | 2vmv_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 2vmv_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/2vmv ftp://data.pdbj.org/pub/pdb/validation_reports/vm/2vmv | HTTPS FTP |
-Related structure data
Related structure data | 2vmnC 2vmoC 2vmpC 2vmqC 2vmrC 2vmsC 2vmtC 2vmuC 2vmwC 2vmxC 2vmyC 2vmzC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 44184.062 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: 1.7→20 Å / Num. obs: 39616 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.8 / % possible all: 97.6 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1KKJ Resolution: 1.7→19.38 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.867 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.117 / 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: 16.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.38 Å
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Refine LS restraints |
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