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Yorodumi- PDB-6uvi: Crystal structure of alr1298, a pentapeptide repeat protein from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uvi | ||||||
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Title | Crystal structure of alr1298, a pentapeptide repeat protein from Nostoc Pcc 7120, determined at 2.3 Angstrom resolution | ||||||
Components | Alr1298 protein | ||||||
Keywords | UNKNOWN FUNCTION / pentapeptide repeat / protein repeat / five residue right-handed-beta helix | ||||||
Function / homology | Pentapeptide repeats (8 copies) / Pentapeptide repeat / Alr1298 protein Function and homology information | ||||||
Biological species | Nostoc sp. PCC 7120 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kennedy, M.A. / Zhang, R. | ||||||
Citation | Journal: Proteins / Year: 2020 Title: Crystal structure of Alr1298, a pentapeptide repeat protein from the cyanobacterium Nostoc sp. PCC 7120, determined at 2.1 angstrom resolution. Authors: Zhang, R. / Ni, S. / Kennedy, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uvi.cif.gz | 151.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uvi.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 6uvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uvi_validation.pdf.gz | 252.2 KB | Display | wwPDB validaton report |
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Full document | 6uvi_full_validation.pdf.gz | 252.2 KB | Display | |
Data in XML | 6uvi_validation.xml.gz | 920 B | Display | |
Data in CIF | 6uvi_validation.cif.gz | 3.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/6uvi ftp://data.pdbj.org/pub/pdb/validation_reports/uv/6uvi | HTTPS FTP |
-Related structure data
Related structure data | 6omxC 6uv7SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20954.623 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr1298 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YXB7 #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: 2.24 Å3/Da / Density % sol: 45.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→31.32 Å / Num. obs: 22287 / % possible obs: 98.03 % / Redundancy: 2 % / Biso Wilson estimate: 40.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01859 / Rpim(I) all: 0.01859 / Rrim(I) all: 0.02629 / Net I/σ(I): 18.53 |
Reflection shell | Resolution: 2.1→2.21 Å / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 17.7 / Num. unique obs: 22336 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6UV7 Resolution: 2.1→31.32 Å / SU ML: 0.3238 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8294
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→31.32 Å
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Refine LS restraints |
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LS refinement shell |
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