+Open data
-Basic information
Entry | Database: PDB / ID: 2vi9 | ||||||
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Title | Crystal structure of S172AbsSHMT Glycine external aldimine | ||||||
Components | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / SHMT / E53Q / FTHF / ENZYME MEMORY / PYRIDOXAL PHOSPHATE / ONE-CARBON METABOLISM / PLP-DEPENDENT ENZYMES | ||||||
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. / Prakash, V. / Appaji Rao, N. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of S172Absshmt and its Complexes Authors: Rajaram, V. / Bhavani, B.S. / 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 | 2vi9.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vi9.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vi9_validation.pdf.gz | 476.3 KB | Display | wwPDB validaton report |
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Full document | 2vi9_full_validation.pdf.gz | 477.2 KB | Display | |
Data in XML | 2vi9_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 2vi9_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/2vi9 ftp://data.pdbj.org/pub/pdb/validation_reports/vi/2vi9 | HTTPS FTP |
-Related structure data
Related structure data | 2vi8C 2viaC 2vibC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44258.184 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, 207 molecules
#2: Chemical | ChemComp-GLY / | ||||
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#3: Chemical | ChemComp-PLP / | ||||
#4: Chemical | #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 PH7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM GLY |
-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→30 Å / Num. obs: 25285 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1KL1 Resolution: 2→24.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.492 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.187 / 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: 26.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2→24.01 Å
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Refine LS restraints |
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