+Open data
-Basic information
Entry | Database: PDB / ID: 5g1r | ||||||
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Title | Open conformation of Francisella tularensis ClpP at 1.9 A | ||||||
Components | ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT | ||||||
Keywords | HYDROLASE | ||||||
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 | FRANCISELLA TULARENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Diaz-Saez, L. / Hunter, W.N. | ||||||
Citation | Journal: Proteins / Year: 2017 Title: Open and compressed conformations of Francisella tularensis ClpP. Authors: Diaz-Saez, L. / Pankov, G. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g1r.cif.gz | 288 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g1r.ent.gz | 235.5 KB | Display | PDB format |
PDBx/mmJSON format | 5g1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g1r_validation.pdf.gz | 517.2 KB | Display | wwPDB validaton report |
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Full document | 5g1r_full_validation.pdf.gz | 537.3 KB | Display | |
Data in XML | 5g1r_validation.xml.gz | 62 KB | Display | |
Data in CIF | 5g1r_validation.cif.gz | 89.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/5g1r ftp://data.pdbj.org/pub/pdb/validation_reports/g1/5g1r | HTTPS FTP |
-Related structure data
Related structure data | 5g1qC 5g1sC 3p2lS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 22177.490 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) FRANCISELLA TULARENSIS (bacteria) / Plasmid: MODIFIED PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q5NH47, endopeptidase Clp #2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: RATIO 1:1, 293K, HANGING DROP. RESERVOIR CONDITION: 0.2 M NACL, 30% (V/V) MPD AND 0.1 M SODIUM ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9799 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.04 Å / Num. obs: 117661 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3P2L Resolution: 1.9→98.26 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.883 / SU B: 4.562 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.168 / 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: 21.142 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→98.26 Å
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Refine LS restraints |
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