+Open data
-Basic information
Entry | Database: PDB / ID: 6pbs | ||||||||||||
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Title | Structure of ClpC1-NTD in complex with Ecumicin | ||||||||||||
Components |
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Keywords | CHAPERONE/ANTIBIOTIC / ClpC1-NTD / Ecumicin / ATPase / Mycobacterium tuberculosis / CHAPERONE-ANTIBIOTIC complex | ||||||||||||
Function / homology | Function and homology information protein folding chaperone / peptidoglycan-based cell wall / ATP hydrolysis activity / protein homodimerization activity / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) Nonomuraea sp. MJM5123 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||||||||
Authors | Abad-Zapatero, C. / Wolf, N.M. | ||||||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Structure of the N-terminal domain of ClpC1 in complex with the antituberculosis natural product ecumicin reveals unique binding interactions. Authors: Wolf, N.M. / Lee, H. / Zagal, D. / Nam, J.W. / Oh, D.C. / Lee, H. / Suh, J.W. / Pauli, G.F. / Cho, S. / Abad-Zapatero, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pbs.cif.gz | 425.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pbs.ent.gz | 359.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/6pbs ftp://data.pdbj.org/pub/pdb/validation_reports/pb/6pbs | HTTPS FTP |
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-Related structure data
Related structure data | 6pbaSC 6pbqC 6ucrC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 17529.131 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: clpC1, Rv3596c, MTCY07H7B.26 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPC9 #2: Protein/peptide | #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.36 Å3/Da / Density % sol: 47.82 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M calcium acetate hydrate, 0.1 M Tris, pH 7.0, 20% PEG3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. obs: 79421 / % possible obs: 98.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.041 / Rrim(I) all: 0.098 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.638 / Num. unique obs: 3828 / Rpim(I) all: 0.364 / Rrim(I) all: 0.786 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6pba Resolution: 2.5→40 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
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Displacement parameters | Biso mean: 64.05 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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