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Yorodumi- PDB-2q7f: Crystal structure of YrrB: a TPR protein with an unusual peptide-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q7f | ||||||
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Title | Crystal structure of YrrB: a TPR protein with an unusual peptide-binding site | ||||||
Components | YrrB protein | ||||||
Keywords | PROTEIN BINDING / TPR / YRRB | ||||||
Function / homology | Function and homology information Tetratricopeptide repeat 2 / Tetratricopeptide repeat / : / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Tetratricopeptide repeat 2 / Tetratricopeptide repeat / : / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å | ||||||
Authors | Oh, J. / Han, D. / Kim, K. / Lim, H. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2007 Title: Crystal structure of YrrB: A TPR protein with an unusual peptide-binding site Authors: Han, D. / Oh, J. / Kim, K. / Lim, H. / Kim, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q7f.cif.gz | 88 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q7f.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 2q7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/2q7f ftp://data.pdbj.org/pub/pdb/validation_reports/q7/2q7f | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 43 - 236 / Label seq-ID: 42 - 235
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-Components
#1: Protein | Mass: 27142.504 Da / Num. of mol.: 2 / Fragment: sequence database residues 4-202 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yrrB / Plasmid: PET 28A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON PLUS RIL / References: UniProt: O34452 #2: 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: 2.1 Å3/Da / Density % sol: 40.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 4.8 Details: 40MM PHOTASSIUM PHOSPHATE(KH2PO4), 4% PEG 6000, 20% GLYCEROL, PH 4.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 4.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9794 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→30 Å / Num. obs: 14817 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.091 |
Reflection shell | Resolution: 2.49→2.59 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1183 / % possible all: 76.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.49→28.48 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 22.117 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.004 / ESU R Free: 0.324 / 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: 59.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→28.48 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.49→2.55 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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