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Yorodumi- PDB-1yjz: K226M Mutant Of Serine Hydroxymethyltransferase From B. Stearothe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yjz | ||||||
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Title | K226M Mutant Of Serine Hydroxymethyltransferase From B. Stearothermophilus | ||||||
Components | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / SHMT / Mutant / Catalysis | ||||||
Function / homology | Function and homology information glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Bhavani, S. / Trivedi, V. / Jala, V.R. / Subramanya, H.S. / Kaul, P. / Purnima, K. / Prakash, V. / Appaji, R.N. / Savithri, H.S. | ||||||
Citation | Journal: Biochemistry / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yjz.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yjz.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 1yjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/1yjz ftp://data.pdbj.org/pub/pdb/validation_reports/yj/1yjz | HTTPS FTP |
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-Related structure data
Related structure data | 1yjsC 1yjyC 1kkjS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | The second part of the biological assembly is generated by the two fold axis : -X, -Y, Z. |
-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.) Geobacillus stearothermophilus (bacteria) Gene: SHMT / Plasmid: PRSETC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q7SIB6, glycine hydroxymethyltransferase |
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#2: Chemical | ChemComp-PLP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.19 % |
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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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 2003 / 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: 22373 / Num. obs: 22373 / % possible obs: 84.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.084 / Num. unique all: 1945 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KKJ Resolution: 2.1→10 Å / Isotropic thermal model: Anisotrophic / σ(I): 3
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å / Rfactor Rfree error: 0.21477
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