+Open data
-Basic information
Entry | Database: PDB / ID: 5dl1 | ||||||
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Title | ClpP from Staphylococcus aureus in complex with AV145 | ||||||
Components | ATP-dependent Clp protease proteolytic subunit | ||||||
Keywords | HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex / caseinolytic protease / allosteric regulation / binding analysis | ||||||
Function / homology | Function and homology information endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Vielberg, M.-T. / Groll, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Reversible Inhibitors Arrest ClpP in a Defined Conformational State that Can Be Revoked by ClpX Association. Authors: Pahl, A. / Lakemeyer, M. / Vielberg, M.T. / Hackl, M.W. / Vomacka, J. / Korotkov, V.S. / Stein, M.L. / Fetzer, C. / Lorenz-Baath, K. / Richter, K. / Waldmann, H. / Groll, M. / Sieber, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dl1.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5dl1.ent.gz | 886.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dl1_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 5dl1_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 5dl1_validation.xml.gz | 99.1 KB | Display | |
Data in CIF | 5dl1_validation.cif.gz | 117.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/5dl1 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dl1 | HTTPS FTP |
-Related structure data
Related structure data | 3v5eS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 21536.531 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: clpP, SAB0722 / Plasmid: pET301 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q2YSF8, UniProt: Q2G036*PLUS, endopeptidase Clp #2: Chemical | ChemComp-5C2 / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 200 mM KNO3, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 56975 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 3→3.1 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V5E Resolution: 3→15 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.913 / SU B: 73.661 / SU ML: 0.564 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 116.775 Å2
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Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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