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Yorodumi- PDB-2x8p: Crystal Structure of CbpF in Complex with Atropine by Co- Crystal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x8p | ||||||
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Title | Crystal Structure of CbpF in Complex with Atropine by Co- Crystallization | ||||||
Components | CHOLINE-BINDING PROTEIN F | ||||||
Keywords | CHOLINE-BINDING PROTEIN / LIPID-BINDING-PROTEIN | ||||||
Function / homology | Function and homology information left handed beta-beta-3-solenoid - #20 / Cholin Binding / left handed beta-beta-3-solenoid / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Ribbon / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Silva-Martin, N. / Hermoso, J.A. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Crystal Structures of Cbpf Complexed with Atropine and Ipratropium Reveal Clues for the Design of Novel Antimicrobials Against Streptococcus Pneumoniae. Authors: Silva-Martin, N. / Retamosa, M.G. / Maestro, B. / Bartual, S.G. / Rodes, M.J. / Garcia, P. / Sanz, J.M. / Hermoso, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x8p.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x8p.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 2x8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x8p_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2x8p_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2x8p_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 2x8p_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/2x8p ftp://data.pdbj.org/pub/pdb/validation_reports/x8/2x8p | HTTPS FTP |
-Related structure data
Related structure data | 2x8mC 2v05S S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36322.938 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PIN-III-A3 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8DR52 |
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-Non-polymers , 5 types, 284 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CHT / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 13 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.12 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: MARRESEARCH / Wavelength: 1.54179 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→24.73 Å / Num. obs: 16653 / % possible obs: 79.5 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 2.1 |
Reflection shell | Resolution: 2.27→2.43 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 79.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V05 Resolution: 2.27→24.73 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2073491.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.16 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.27→24.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.27→2.41 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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