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Yorodumi- PDB-4ig4: Crystal structure of single mutant thermostable NPPase (N86S) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ig4 | ||||||
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Title | Crystal structure of single mutant thermostable NPPase (N86S) from Geobacillus stearothermophilus | ||||||
Components | Thermostable NPPase | ||||||
Keywords | HYDROLASE / thermostable NPPase | ||||||
Function / homology | Function and homology information phosphoglycolate phosphatase activity / alkaline phosphatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å | ||||||
Authors | Guo, Z. / Wang, F. / Huang, J. / Qiu, R. / Yang, Z. / Wang, Y. / Gong, W. / Ji, C. | ||||||
Citation | Journal: To be Published Title: Crystal structure of thermostable NPPase from Geobacillus stearothermophilus Authors: Guo, Z. / Wang, F. / Huang, J. / Qiu, R. / Yang, Z. / Wang, Y. / Ji, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ig4.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ig4.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ig4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ig4_validation.pdf.gz | 433.6 KB | Display | wwPDB validaton report |
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Full document | 4ig4_full_validation.pdf.gz | 437.3 KB | Display | |
Data in XML | 4ig4_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 4ig4_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/4ig4 ftp://data.pdbj.org/pub/pdb/validation_reports/ig/4ig4 | HTTPS FTP |
-Related structure data
Related structure data | 4iftSC 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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Unit cell |
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-Components
#1: Protein | Mass: 29663.730 Da / Num. of mol.: 2 / Mutation: N86S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: Q8L1N9 #2: 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: 2.4 Å3/Da / Density % sol: 48.71 % / Mosaicity: 0.526 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES sodium, 2.0M Ammonium sulfate, 3% PEG400, 30% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 1, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. all: 22962 / Num. obs: 22962 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.19 / Χ2: 4.067 / Net I/σ(I): 6.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IFT Resolution: 2.402→41.643 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8184 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 24.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.47 Å2 / Biso mean: 42.8939 Å2 / Biso min: 12.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.402→41.643 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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