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Yorodumi- PDB-5zdi: Crystal structure of CsaA chaperone protein from picrophilus torridus -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zdi | ||||||
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Title | Crystal structure of CsaA chaperone protein from picrophilus torridus | ||||||
Components | Protein secretion chaperonin CsaA | ||||||
Keywords | CHAPERONE / tRNA-binding protein / Thermoacidophiles | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Picrophilus torridus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kumari, S. / Sharma, A. / Goel, M. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of CsaA chaperone protein from picrophilus torridus Authors: Sharma, A. / Kumari, S. / Verma, V. / Goel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zdi.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zdi.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 5zdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zdi_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
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Full document | 5zdi_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | 5zdi_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 5zdi_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/5zdi ftp://data.pdbj.org/pub/pdb/validation_reports/zd/5zdi | HTTPS FTP |
-Related structure data
Related structure data | 2nzhS 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: 11806.739 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828) (archaea) Strain: ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828 / Gene: PTO0409 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6L208 #2: Chemical | ChemComp-GOL / | #3: 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 meas: 2.41 Mg/m3 / Density % sol: 49.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20mM Tris buffer pH 8.0, 0.2 M ammonium sul-phate, 1 M NaCl, 25% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 25764 / % possible obs: 98 % / Redundancy: 7.3 % / Χ2: 1.489 / Net I/σ(I): 24.96 |
Reflection shell | Resolution: 1.7→1.76 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NZH Resolution: 1.7→49.43 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.426 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.11 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.063 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→49.43 Å
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Refine LS restraints |
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