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Yorodumi- PDB-3i9x: Crystal structure of a mutT/nudix family protein from Listeria innocua -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i9x | ||||||
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Title | Crystal structure of a mutT/nudix family protein from Listeria innocua | ||||||
Components | mutT/nudix family protein | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Listeria innocua (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Miller, S. / Romero, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a mutT/nudix family protein from Listeria innocua Authors: Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Miller, S. / Romero, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i9x.cif.gz | 44.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i9x.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 3i9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i9x_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 3i9x_full_validation.pdf.gz | 429 KB | Display | |
Data in XML | 3i9x_validation.xml.gz | 8 KB | Display | |
Data in CIF | 3i9x_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/3i9x ftp://data.pdbj.org/pub/pdb/validation_reports/i9/3i9x | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | possible dimer |
-Components
#1: Protein | Mass: 20924.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin0490 / Plasmid: modified pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92EH0 |
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#2: Chemical | ChemComp-GOL / |
#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: 3.11 Å3/Da / Density % sol: 60.46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7.5 Details: 100mM Hepes pH 7.5, 4% glycerol, 1.3M tri-sodium citrate, vapor diffusion, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2009 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→31.668 Å / Num. all: 14089 / Num. obs: 14075 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 42.4 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 43.3 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 9.9 / Num. unique all: 2001 / Rsym value: 0.449 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.295 / WRfactor Rwork: 0.239 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.813 / SU B: 5.018 / SU ML: 0.13 / SU R Cruickshank DPI: 0.191 / SU Rfree: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.191 / ESU R Free: 0.188 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.97 Å2 / Biso mean: 50.271 Å2 / Biso min: 31.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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