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Yorodumi- PDB-3tla: Microcin C7 self immunity protein MccF in the wild type APO state -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tla | ||||||
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Title | Microcin C7 self immunity protein MccF in the wild type APO state | ||||||
Components | MccF | ||||||
Keywords | HYDROLASE / serine protease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.201 Å | ||||||
Authors | Agarwal, V. / Nair, S.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structure and function of a serine carboxypeptidase adapted for degradation of the protein synthesis antibiotic microcin C7. Authors: Agarwal, V. / Tikhonov, A. / Metlitskaya, A. / Severinov, K. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tla.cif.gz | 166 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tla.ent.gz | 127.6 KB | Display | PDB format |
PDBx/mmJSON format | 3tla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tla_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
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Full document | 3tla_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 3tla_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 3tla_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/3tla ftp://data.pdbj.org/pub/pdb/validation_reports/tl/3tla | HTTPS FTP |
-Related structure data
Related structure data | 3tlbC 3tlcC 3tleC 3tlgC 3tlyC 3tlzC 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: 41732.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mccF / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2KKH9, UniProt: Q47511*PLUS #2: Chemical | ChemComp-EDO / | #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: 2.01 Å3/Da / Density % sol: 38.73 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 8000, 8% ethylene glycol, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→50 Å / Num. obs: 202577 / % possible obs: 98.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.068 / Χ2: 1.324 / Net I/σ(I): 9.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.201→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 0.584 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.044 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.81 Å2 / Biso mean: 13.3085 Å2 / Biso min: 6.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.201→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.201→1.232 Å / Total num. of bins used: 20
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