+Open data
-Basic information
Entry | Database: PDB / ID: 5nyq | ||||||
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Title | Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 - SG:R32 | ||||||
Components | Anbu | ||||||
Keywords | HYDROLASE / Ntn-hydrolase-fold / proteasome / evolution | ||||||
Function / homology | Uncharacterised conserved protein UCP009120, proteasome-type protease, Sll0069 / proteasome core complex / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / proteolysis involved in protein catabolic process / PHOSPHATE ION / Peptidase Function and homology information | ||||||
Biological species | Hyphomicrobium sp. | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Vielberg, M.-T. / Groll, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J. Mol. Biol. / Year: 2018 Title: On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral beta-Subunit Protein Anbu. Authors: Vielberg, M.T. / Bauer, V.C. / Groll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nyq.cif.gz | 102.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nyq.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 5nyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nyq_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 5nyq_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 5nyq_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 5nyq_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/5nyq ftp://data.pdbj.org/pub/pdb/validation_reports/ny/5nyq | HTTPS FTP |
-Related structure data
Related structure data | 5nyfSC 5nygC 5nyjC 5nypC 5nyrC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27536.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hyphomicrobium sp. (strain MC1) (bacteria) Gene: HYPMC_4374 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8JB59 | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.52 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.8 M sodium phosphate, 0.8 M potassium phosphate, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. obs: 17067 / % possible obs: 99.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 1.95→2.05 Å / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 4.27 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NYF Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.376 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.698 / ESU R Free: 0.14 / 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: 43.418 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→20 Å
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Refine LS restraints |
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