[English] 日本語
Yorodumi- PDB-3tlb: Microcin C7 self immunity protein MccF in complex aspartyl sulfam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tlb | ||||||
---|---|---|---|---|---|---|---|
Title | Microcin C7 self immunity protein MccF in complex aspartyl sulfamoyl adenosine | ||||||
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: 1.501 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3tlb.cif.gz | 162.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3tlb.ent.gz | 125.4 KB | Display | PDB format |
PDBx/mmJSON format | 3tlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tlb_validation.pdf.gz | 979.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3tlb_full_validation.pdf.gz | 981.5 KB | Display | |
Data in XML | 3tlb_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 3tlb_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/3tlb ftp://data.pdbj.org/pub/pdb/validation_reports/tl/3tlb | HTTPS FTP |
-Related structure data
Related structure data | 3tlaSC 3tlcC 3tleC 3tlgC 3tlyC 3tlzC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41716.586 Da / Num. of mol.: 2 / Mutation: S168A 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.4 % |
---|---|
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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 99681 / % possible obs: 95.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.058 / Χ2: 0.877 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TLA Resolution: 1.501→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.225 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 500 Å2 / Biso mean: 14.5943 Å2 / Biso min: 6.19 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.501→25 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
|