+Open data
-Basic information
Entry | Database: PDB / ID: 4gdn | ||||||
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Title | Structure of FmtA-like protein | ||||||
Components | Protein flp | ||||||
Keywords | HYDROLASE / peptidase / alpha/beta | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Cougnoux, A. / Gibold, L. / Delmas, J. / Robin, F. / Dalmasso, G. / Bonnet, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Analysis of Structure-Function Relationships in the Colibactin-Maturating Enzyme ClbP. Authors: Cougnoux, A. / Gibold, L. / Robin, F. / Dubois, D. / Pradel, N. / Darfeuille-Michaud, A. / Dalmasso, G. / Delmas, J. / Bonnet, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gdn.cif.gz | 264.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gdn.ent.gz | 215.7 KB | Display | PDB format |
PDBx/mmJSON format | 4gdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gdn_validation.pdf.gz | 774.1 KB | Display | wwPDB validaton report |
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Full document | 4gdn_full_validation.pdf.gz | 855.5 KB | Display | |
Data in XML | 4gdn_validation.xml.gz | 55.1 KB | Display | |
Data in CIF | 4gdn_validation.cif.gz | 74.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/4gdn ftp://data.pdbj.org/pub/pdb/validation_reports/gd/4gdn | HTTPS FTP |
-Related structure data
Related structure data | 3o3vS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 38702.395 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: flp, SA2230 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7A3Q5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds #2: Chemical | ChemComp-PE4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2M ammonium acetate, 0.1M sodium acetate trihydrate, 30% W/v polyethylene glycol 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2011 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→85.76 Å / Num. obs: 42000 / % possible obs: 97.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.2 / Num. unique all: 42000 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3O3V Resolution: 3.2→85.73 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.842 / Cross valid method: THROUGHOUT / ESU R Free: 0.49 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.071 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→85.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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