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Yorodumi- PDB-5cec: Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cec | |||||||||
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Title | Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460 | |||||||||
Components |
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Keywords | PROTEIN BINDING / transpeptidase and ankyrin repeat | |||||||||
Function / homology | Function and homology information serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / proteolysis Similarity search - Function | |||||||||
Biological species | Bdellovibrio bacteriovorus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | |||||||||
Authors | Lovering, A.L. / Cadby, I.T. / Lambert, C. / Sockett, R.E. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2015 Title: Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus. Authors: Lambert, C. / Cadby, I.T. / Till, R. / Bui, N.K. / Lerner, T.R. / Hughes, W.S. / Lee, D.J. / Alderwick, L.J. / Vollmer, W. / Sockett, E.R. / Lovering, A.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cec.cif.gz | 261.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cec.ent.gz | 208 KB | Display | PDB format |
PDBx/mmJSON format | 5cec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/5cec ftp://data.pdbj.org/pub/pdb/validation_reports/ce/5cec | HTTPS FTP |
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-Related structure data
Related structure data | 5ceaSC 5cebSC 5cedC 5cerC 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
#1: Protein | Mass: 49219.406 Da / Num. of mol.: 1 / Fragment: Bd3459 / Mutation: K38M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria) Gene: Bd3459 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q6MHT0, serine-type D-Ala-D-Ala carboxypeptidase | ||
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#2: Protein | Mass: 24755.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria) Gene: Bd3460 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6MHS9 | ||
#3: Chemical | ChemComp-SO4 / #4: 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: 1.98 Å3/Da / Density % sol: 38.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M citrate pH 5.0, 3.2M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→100 Å / Num. obs: 117291 / % possible obs: 97.2 % / Redundancy: 6 % / Rsym value: 0.032 / Net I/σ(I): 23.4 |
Reflection shell | Rsym value: 0.516 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CEA & 5CEB Resolution: 1.36→96.14 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.737 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 92.9 Å2 / Biso mean: 23.69 Å2 / Biso min: 12.22 Å2
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Refinement step | Cycle: final / Resolution: 1.36→96.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.395 Å / Total num. of bins used: 20
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