+Open data
-Basic information
Entry | Database: PDB / ID: 1pug | ||||||
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Title | Structure of E. coli Ybab | ||||||
Components | Hypothetical UPF0133 protein ybaB | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NYSGXRC T5 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.2 Å | ||||||
Authors | Kniewel, R. / Buglino, J. / Chadna, T. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Structure of E. coli Ybab Authors: Kniewel, R. / Buglino, J. / Chadna, T. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pug.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pug.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pug_validation.pdf.gz | 449.4 KB | Display | wwPDB validaton report |
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Full document | 1pug_full_validation.pdf.gz | 466.1 KB | Display | |
Data in XML | 1pug_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 1pug_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/1pug ftp://data.pdbj.org/pub/pdb/validation_reports/pu/1pug | 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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Unit cell |
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Details | APPARENT DIMER (A,B) AND (C,D) ALSO BY GEL FILTRATION |
-Components
#1: Protein | Mass: 12028.819 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YBAB / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: P0A8B5 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 1.9M Ammonium Sulfate 0.1MSodium HEPES pH 7.5 5% Ethylene Glycol, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 28, 2003 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 37158 / Num. obs: 36898 / % possible obs: 99.3 % / Observed criterion σ(I): -0.5 / Rmerge(I) obs: 0.073 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.202 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.217 / Stereochemistry target values: Engh & Huber / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.383 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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