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Yorodumi- PDB-4ij5: Crystal Structure of a Novel-type Phosphoserine Phosphatase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ij5 | ||||||
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Title | Crystal Structure of a Novel-type Phosphoserine Phosphatase from Hydrogenobacter thermophilus TK-6 | ||||||
Components | Phosphoserine phosphatase 1 | ||||||
Keywords | HYDROLASE / phosphatase | ||||||
Function / homology | Function and homology information phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process Similarity search - Function | ||||||
Biological species | Hydrogenobacter thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Chiba, Y. / Horita, S. / Ohtsuka, J. / Arai, H. / Nagata, K. / Igarashi, Y. / Tanokura, M. / Ishii, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis Authors: Chiba, Y. / Horita, S. / Ohtsuka, J. / Arai, H. / Nagata, K. / Igarashi, Y. / Tanokura, M. / Ishii, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ij5.cif.gz | 183.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ij5.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ij5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/4ij5 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/4ij5 | HTTPS FTP |
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-Related structure data
Related structure data | 4ij6C 1h2eS 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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-Components
#1: Protein | Mass: 24593.346 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria) Strain: DSM 6534 / IAM 12695 / TK-6 / Gene: pspA, pgmA, HTH_0103, Hydth_0104 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DFG8, phosphoserine phosphatase #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM HEPES-NaOH, 10%(v/v) 2-propanol, 20%(w/v) polyethylene glycol 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: MAR225HE / Detector: CCD / Date: Jul 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→36.1 Å / Num. all: 73684 / Num. obs: 73612 / Redundancy: 8.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H2E Resolution: 1.5→36.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.461 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 41.06 Å2 / Biso mean: 16.45 Å2 / Biso min: 3.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→36.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.541 Å / Total num. of bins used: 20
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Refinement TLS params. | S33: -0.0049 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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