+Open data
-Basic information
Entry | Database: PDB / ID: 5loy | ||||||
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Title | Helical Assembly of a Designed Anbu Protein | ||||||
Components | Designed Anbu Protein | ||||||
Keywords | HYDROLASE / Protein Degradation / Ancestral Beta Subunit / Proteasome Precursor / Consensus Design / METAL BINDING PROTEIN | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Fuchs, A.C.D. / Albrecht, R. / Martin, J. / Hartmann, M.D. | ||||||
Citation | Journal: Structure / Year: 2017 Title: The Architecture of the Anbu Complex Reflects an Evolutionary Intermediate at the Origin of the Proteasome System. Authors: Fuchs, A.C.D. / Alva, V. / Maldoner, L. / Albrecht, R. / Hartmann, M.D. / Martin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5loy.cif.gz | 369.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5loy.ent.gz | 304.4 KB | Display | PDB format |
PDBx/mmJSON format | 5loy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5loy_validation.pdf.gz | 441.9 KB | Display | wwPDB validaton report |
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Full document | 5loy_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 5loy_validation.xml.gz | 35 KB | Display | |
Data in CIF | 5loy_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/5loy ftp://data.pdbj.org/pub/pdb/validation_reports/lo/5loy | HTTPS FTP |
-Related structure data
Related structure data | 5loxSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 1 - 239 / Label seq-ID: 1 - 239
NCS ensembles :
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-Components
#1: Protein | Mass: 26744.281 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Manually created consensus sequence based on a multiple sequence alignment of Anbu proteins Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #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: 3.14 Å3/Da / Density % sol: 60.81 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES-NaOH pH 7.0, 0.6 M NaF |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→38.7 Å / Num. obs: 47607 / % possible obs: 99.8 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Net I/σ(I): 18.96 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.789 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LOX Resolution: 2.5→38.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 15.083 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.23 / 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: 47.019 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→38.7 Å
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Refine LS restraints |
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