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Yorodumi- PDB-3tle: Microcin C7 self immunity protein MccF in complex with glutamyl s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tle | ||||||
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Title | Microcin C7 self immunity protein MccF in complex with glutamyl sulfamoyl adenylate | ||||||
Components | MccF | ||||||
Keywords | HYDROLASE / serine protease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 | 3tle.cif.gz | 166.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tle.ent.gz | 127.5 KB | Display | PDB format |
PDBx/mmJSON format | 3tle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tle_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3tle_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3tle_validation.xml.gz | 35 KB | Display | |
Data in CIF | 3tle_validation.cif.gz | 55 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/3tle ftp://data.pdbj.org/pub/pdb/validation_reports/tl/3tle | HTTPS FTP |
-Related structure data
Related structure data | 3tlaSC 3tlbC 3tlcC 3tlgC 3tlyC 3tlzC 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: 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 | #3: Chemical | ChemComp-EDO / | #4: 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 Å3/Da / Density % sol: 38.52 % |
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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 | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→71.6 Å / Num. obs: 157419 / % possible obs: 98.2 % / Redundancy: 3.8 % / Rsym value: 0.061 / Net I/σ(I): 36.9 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 9.5 / Rsym value: 0.217 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TLA Resolution: 1.3→25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 1 / SU B: 0.699 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 12.749 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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