[English] 日本語
Yorodumi- PDB-4fwg: Crystal structure of the Lon-like protease MtaLonC in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fwg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Lon-like protease MtaLonC in complex with lactacystin | ||||||
Components | TTC1975 peptidase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Lon protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information endopeptidase La / ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / proteolysis / ATP binding Similarity search - Function | ||||||
Biological species | Meiothermus taiwanensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Chang, C.I. / Kuo, C.I. / Huang, K.F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors Authors: Liao, J.H. / Ihara, K. / Kuo, C.I. / Huang, K.F. / Wakatsuki, S. / Wu, S.H. / Chang, C.I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4fwg.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4fwg.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fwg_validation.pdf.gz | 466.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4fwg_full_validation.pdf.gz | 489.6 KB | Display | |
Data in XML | 4fwg_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 4fwg_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/4fwg ftp://data.pdbj.org/pub/pdb/validation_reports/fw/4fwg | HTTPS FTP |
-Related structure data
Related structure data | 4fw9SC 4fwdC 4fwhC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 6||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 81067.492 Da / Num. of mol.: 1 / Mutation: L91M, L188M, I359M, L390M, Y557M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C9DRU9, endopeptidase La |
---|---|
#2: Chemical | ChemComp-SLA / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.98 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 10% isopropanol, 200mM di-potassium phosphate, 100mM sodium citrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å | |||||||||||||||
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: Jun 10, 2011 | |||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 1.94→20 Å / Num. all: 76153 / Num. obs: 75772 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 13.4 | |||||||||||||||
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 7 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 2.7 / Num. unique all: 7603 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FW9 Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.718 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 37.063 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.989→2.04 Å / Total num. of bins used: 20
|