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Yorodumi- PDB-4fwd: Crystal structure of the Lon-like protease MtaLonC in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fwd | ||||||
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Title | Crystal structure of the Lon-like protease MtaLonC in complex with bortezomib | ||||||
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: 2.03 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fwd.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fwd.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 4fwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/4fwd ftp://data.pdbj.org/pub/pdb/validation_reports/fw/4fwd | HTTPS FTP |
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-Related structure data
Related structure data | 4fw9SC 4fwgC 4fwhC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 80558.352 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-BO2 / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.4 % |
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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 | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 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 |
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Reflection | Resolution: 2.02→50 Å / Num. all: 67494 / Num. obs: 65537 / % possible obs: 97.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 24.6 | |||||||||||||||
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6268 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FW9 Resolution: 2.03→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.039 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 40.921 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.029→2.082 Å / Total num. of bins used: 20
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