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- PDB-1yjy: K226M Mutant Of Serine Hydroxymethyltransferase From B. Stearothe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yjy | ||||||
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Title | K226M Mutant Of Serine Hydroxymethyltransferase From B. Stearothermophilus, Complex With Serine | ||||||
![]() | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
![]() | TRANSFERASE / SHMT / Mutant / Catalysis | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bhavani, S. / Trivedi, V. / Jala, V.R. / Subramanya, H.S. / Kaul, P. / Purnima, K. / Prakash, V. / Appaji, R.N. / Savithri, H.S. | ||||||
![]() | ![]() Title: Role of Lys-226 in the Catalytic Mechanism of Bacillus Stearothermophilus Serine Hydroxymethyltransferase-Crystal Structure and Kinetic Studies Authors: Bhavani, S. / Trivedi, V. / Jala, V.R. / Subramanya, H.S. / Kaul, P. / Purnima, K. / Prakash, V. / Appaji, R.N. / Savithri, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.4 KB | Display | ![]() |
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PDB format | ![]() | 70 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.4 KB | Display | ![]() |
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Full document | ![]() | 460.7 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yjsC ![]() 1yjzC ![]() 1kkjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis : -X, -Y, Z. |
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Components
#1: Protein | Mass: 45713.754 Da / Num. of mol.: 1 / Fragment: Serine methylase / Mutation: K226M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SHMT / Plasmid: PRSETC / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: Q7SIB6, glycine hydroxymethyltransferase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-SER / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Hepes, MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 11, 2002 / Details: 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: 2.1→15 Å / Num. all: 18477 / Num. obs: 18477 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 2 % / Rmerge(I) obs: 0.145 / Num. unique all: 1782 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KKJ Resolution: 2.25→10 Å / Isotropic thermal model: Anisotrophic / σ(F): 0 / σ(I): 3
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Refinement step | Cycle: LAST / Resolution: 2.25→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.33 Å / Rfactor Rfree error: 0.19808
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