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Yorodumi- PDB-2fi0: The crystal structure of the conserved domain protein from Strept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fi0 | ||||||
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Title | The crystal structure of the conserved domain protein from Streptococcus pneumoniae TIGR4 | ||||||
Components | conserved domain proteinProtein domain | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Streptococcus pneumoniae / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | SP0561-like / SP0561-like / Domain of unknown function DUF1858 / ScdA-like, N-terminal domain superfamily / Domain of unknown function (DUF1858) / Orthogonal Bundle / Mainly Alpha / : / DUF1858 domain-containing protein Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Zhang, R. / Li, H. / Abdullah, J. / Collart, F. / Cymborowski, M. / Minor, W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the conserved domain protein from Streptococcus pneumoniae TIGR4 Authors: Zhang, R. / Li, H. / Abdullah, J. / Collart, F. / Cymborowski, M. / Minor, W. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fi0.cif.gz | 27.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fi0.ent.gz | 18.4 KB | Display | PDB format |
PDBx/mmJSON format | 2fi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/2fi0 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/2fi0 | HTTPS FTP |
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-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
#1: Protein | Mass: 8865.405 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 14972036, UniProt: Q8CZ42*PLUS |
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#2: 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: 3.83 Å3/Da / Density % sol: 67.89 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.5 M NaCl, 0.1M Tris-HCl, 0.2M MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 7362 / Num. obs: 6747 / % possible obs: 91.64 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.77 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1572 / % possible all: 43.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→46.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.944 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.162 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.344 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→46.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 36.321 Å / Origin y: 12.599 Å / Origin z: 19.019 Å
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Refinement TLS group |
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