[English] 日本語
Yorodumi- PDB-4fca: The crystal structure of a functionally unknown conserved protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fca | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of a functionally unknown conserved protein from Bacillus anthracis str. Ames. | ||||||
Components | Conserved domain protein | ||||||
Keywords | Structural Genomics / Unknown Function / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases | ||||||
Function / homology | Function and homology information Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin-like domain 1 / Immunoglobulin-like - #3600 / Peptidase M60, enhancin-like domain 2 / M60-like domain, N-terminal / N-terminal domain of M60-like peptidases / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. ...Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin-like domain 1 / Immunoglobulin-like - #3600 / Peptidase M60, enhancin-like domain 2 / M60-like domain, N-terminal / N-terminal domain of M60-like peptidases / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Neutral Protease; domain 2 / Collagenase (Catalytic Domain) / Jelly Rolls / Immunoglobulin-like / Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.055 Å | ||||||
Authors | Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a functionally unknown conserved protein from Bacillus anthracis str. Ames. Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4fca.cif.gz | 208.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4fca.ent.gz | 173.8 KB | Display | PDB format |
PDBx/mmJSON format | 4fca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fca_validation.pdf.gz | 442 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4fca_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 4fca_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 4fca_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/4fca ftp://data.pdbj.org/pub/pdb/validation_reports/fc/4fca | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | Experimentally unknown. It is predicted to be monomeric. |
-Components
#1: Protein | Mass: 60880.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS4929, BA_5305 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81XD4, UniProt: A0A0F7RB18*PLUS |
---|---|
#2: Chemical | ChemComp-IMD / |
#3: Chemical | ChemComp-NI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.98 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.16M Magnesium Chloride, 0.08M Tris:HCl, 24% (w/v) PEG4000, 20% (v/v) Glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2012 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→29 Å / Num. all: 34563 / Num. obs: 34563 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1704 / % possible all: 99.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.055→28.673 Å / SU ML: 0.63 / σ(F): 1.33 / Phase error: 32.39 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.066 Å2 / ksol: 0.294 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.055→28.673 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|