+Open data
-Basic information
Entry | Database: PDB / ID: 3c9p | ||||||
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Title | Crystal structure of uncharacterized protein SP1917 | ||||||
Components | Uncharacterized protein SP1917 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Streptococcus pneumoniae / SP_1917 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | uncharacterized protein sp1917 domain / Uncharacterised conserved protein UCP033199 / SP1917 domain superfamily / Uncharacterized protein conserved in bacteria (DUF2200) / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å | ||||||
Authors | Chang, C. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of uncharacterized protein SP1917. Authors: Chang, C. / Zhou, M. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c9p.cif.gz | 37.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c9p.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 3c9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c9p_validation.pdf.gz | 418.7 KB | Display | wwPDB validaton report |
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Full document | 3c9p_full_validation.pdf.gz | 418.7 KB | Display | |
Data in XML | 3c9p_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 3c9p_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/3c9p ftp://data.pdbj.org/pub/pdb/validation_reports/c9/3c9p | 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
#1: Protein | Mass: 14277.993 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1917 / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q97NU5, UniProt: A5MA43*PLUS |
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#2: Chemical | ChemComp-EDO / |
#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: 2.18 Å3/Da / Density % sol: 43.55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.7M Sodium citrate tribasic dihydrate, 0.1M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2007 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. all: 9499 / Num. obs: 9480 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 16.65 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 8 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 5.18 / Num. unique all: 921 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.96→37.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.827 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.149 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.329 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→37.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.01 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 30.8945 Å / Origin y: 1.8145 Å / Origin z: 4.571 Å
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