+Open data
-Basic information
Entry | Database: PDB / ID: 1y88 | ||||||
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Title | Crystal Structure of Protein of Unknown Function AF1548 | ||||||
Components | Hypothetical protein AF1548 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / AF1548 / APC5567 / Protein Structure Initiative / PSI / Midwest Center for Structural Genomics Center / MCSG | ||||||
Function / homology | Function and homology information DNA restriction-modification system / endonuclease activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å | ||||||
Authors | Lunin, V.V. / Evdokimova, E. / Kudritskaya, M. / Cuff, M.E. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of hypothetical protein AF1548 from Archaeoglobus fulgidus Authors: Lunin, V.V. / Evdokimova, E. / Kudritskaya, M. / Cuff, M.E. / Joachimiak, A. / Edwards, A. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y88.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y88.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 1y88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y88_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 1y88_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 1y88_validation.xml.gz | 11 KB | Display | |
Data in CIF | 1y88_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/1y88 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/1y88 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | The second part of the biological assembly is generated by the two fold axis: Y, X, -Z |
-Components
#1: Protein | Mass: 22605.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O28724 | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Chemical | ChemComp-SO4 / #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: 3.5 Å3/Da / Density % sol: 65 % Description: The original data collected includes freidel pairs thus the number of reflection reported in the data collection is almost twice that used in the refinement |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M (NH4)2SO4, 15% PEG 3350, 2% PEG 400, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Oct 29, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 46454 / Num. obs: 46443 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.85→1.92 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.378 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.582 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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