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Yorodumi- PDB-5cyb: Structure of a lipocalin lipoprotein affecting virulence in Strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cyb | |||||||||
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Title | Structure of a lipocalin lipoprotein affecting virulence in Streptococcus pneumoniae | |||||||||
Components | Lipoprotein | |||||||||
Keywords | TRANSPORT PROTEIN / lipocalin / lipoprotein / PccL / virulence | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptococcus pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Carrasco-Lopez, C. / Abdullah, M.R. / Hammerschmidt, S. / Hermoso, J.A. | |||||||||
Funding support | Spain, Germany, 2items
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Citation | Journal: To Be Published Title: Unraveling the function and structure of a lipocalin lipoprotein affecting virulence in Streptococcus pneumoniae Authors: Abdullah, M.R. / Carrasco-Lopez, C. / Saleh, M. / Gomez, A. / Petruschka, L. / VoB, F. / Pribyl, T. / Hermoso, J.A. / Hammerschmidt, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cyb.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cyb.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 5cyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cyb_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
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Full document | 5cyb_full_validation.pdf.gz | 445 KB | Display | |
Data in XML | 5cyb_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 5cyb_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/5cyb ftp://data.pdbj.org/pub/pdb/validation_reports/cy/5cyb | HTTPS FTP |
-Related structure data
Related structure data | 3ge2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16471.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) Gene: ERS019416_00104, ERS019595_00220, ERS021447_05272, ERS022232_05596, ERS409134_00058, ERS409372_00175, ERS515225_00124 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0T8N286 | ||
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#2: Chemical | ChemComp-GOL / | ||
#3: Chemical | ChemComp-ACT / | ||
#4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.48 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Na Acetate pH 4.6 0.01 Zn Chloride 18% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.1 Å / Num. obs: 13101 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 7.88 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.52 / % possible all: 89.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GE2 Resolution: 2.1→41.1 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.46 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→41.1 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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