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Yorodumi- PDB-6uv7: Crystal structure of alr1298, a pentapeptide repeat protein from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uv7 | ||||||
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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. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 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 | 6uv7.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uv7.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 6uv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uv7_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 6uv7_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 6uv7_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 6uv7_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/6uv7 ftp://data.pdbj.org/pub/pdb/validation_reports/uv/6uv7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21272.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr1298 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YXB7 #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.25 Å3/Da / Density % sol: 45.32 % |
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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: Oct 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→30.02 Å / Num. obs: 18106 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 55.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02771 / Rpim(I) all: 0.02771 / Rrim(I) all: 0.03918 / Net I/σ(I): 17.18 |
Reflection shell | Resolution: 2.27→2.4 Å / Redundancy: 12.6 % / Num. unique obs: 18173 / CC1/2: 0.999 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.27→30.02 Å / SU ML: 0.3383 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.9811
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→30.02 Å
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Refine LS restraints |
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LS refinement shell |
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