+Open data
-Basic information
Entry | Database: PDB / ID: 2y6y | ||||||
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Title | Crystal structure of TtrD from Archaeoglobus fulgidus | ||||||
Components | CHAPERONE PROTEIN TTRD | ||||||
Keywords | CHAPERONE / TAT SYSTEM | ||||||
Function / homology | TorD-like / TorD-like / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Orthogonal Bundle / Mainly Alpha / cytoplasm / Tat proofreading chaperone TtrD Function and homology information | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dawson, A. / Coulthurst, S.J. / Sargent, F. / Hunter, W.N. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Conserved Signal Peptide Recognition Systems Across the Prokaryotic Domains. Authors: Coulthurst, S.J. / Dawson, A. / Hunter, W.N. / Sargent, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y6y.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y6y.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 2y6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y6y_validation.pdf.gz | 427.2 KB | Display | wwPDB validaton report |
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Full document | 2y6y_full_validation.pdf.gz | 428.5 KB | Display | |
Data in XML | 2y6y_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 2y6y_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/2y6y ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y6y | HTTPS FTP |
-Related structure data
Related structure data | 2xolSC 2yjmC 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
#1: Protein | Mass: 20396.436 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PET15BTEV_TTRD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O30077 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Sequence details | ADDITIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.5 % / Description: NONE |
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Crystal grow | Details: PROTEIN BUFFER 50 MM TRIS, 250 MM NACL, PH 7.5; RESERVOIR 4.3 M NACL, 0.1 M HEPES PH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97698 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97698 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→55.9 Å / Num. obs: 18960 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XOL Resolution: 2.2→55.93 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.177 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.149 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.414 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→55.93 Å
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Refine LS restraints |
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