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Yorodumi- PDB-4ycs: Crystal structure of putative lipoprotein from Peptoclostridium d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ycs | ||||||
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Title | Crystal structure of putative lipoprotein from Peptoclostridium difficile 630 (fragment) | ||||||
Components | Uncharacterized protein | ||||||
Keywords | HYDROLASE / Human Microbiome / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Peptoclostridium difficile 630 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å | ||||||
Authors | Michalska, K. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of putative lipoprotein from Peptoclostridium difficile 630 (fragment) Authors: Michalska, K. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ycs.cif.gz | 301.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ycs.ent.gz | 258.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ycs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/4ycs ftp://data.pdbj.org/pub/pdb/validation_reports/yc/4ycs | 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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Unit cell |
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Details | The biomolecule is unknown |
-Components
#1: Protein | Mass: 14238.272 Da / Num. of mol.: 6 / Fragment: UNP residues 45-169 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptoclostridium difficile 630 (bacteria) Gene: BG47_10265 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: A0A031WBX8, UniProt: Q189B5*PLUS #2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.09 M Malonic Acid, 0.013 M Ammonium Citrate Tribasic, 0.006 M Succinic Acid, 0.015 M DL-Malic Acid, 0.02 M Sodium Acetate, 0.025 M Sodium Formate, 0.008 M Ammonium Tartrate Dibasic, 0.1 M ...Details: 0.09 M Malonic Acid, 0.013 M Ammonium Citrate Tribasic, 0.006 M Succinic Acid, 0.015 M DL-Malic Acid, 0.02 M Sodium Acetate, 0.025 M Sodium Formate, 0.008 M Ammonium Tartrate Dibasic, 0.1 M HEPES:NaOH pH 7.0, 10% (w/v) PEG MME 5000, cryo 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2013 / Details: mirrors |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→30 Å / Num. obs: 57544 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2.25 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.98→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.615 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.151 / 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: 39.857 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→30 Å
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