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Yorodumi- PDB-1rfz: Structure of Protein of Unknown Function from Bacillus stearother... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rfz | ||||||
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Title | Structure of Protein of Unknown Function from Bacillus stearothermophilus | ||||||
Components | Hypothetical protein APC35681 | ||||||
Keywords | Structural Genomics / unknown function / Hypothetical Protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Kim, Y. / Wu, R. / Cuff, M.E. / Quartey, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structure of hypothetical protein APC35681 from Bacillus stearothermophilus Authors: Kim, Y. / Wu, R. / Cuff, M.E. / Quartey, P. / Joachimiak, A. | ||||||
History |
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Remark 999 | SEQUENCE THERE WAS NO DATABASE REFERENCE SEQUENCE FOR THE PROTEIN AT THE TIME OF PROCESSING. ...SEQUENCE THERE WAS NO DATABASE REFERENCE SEQUENCE FOR THE PROTEIN AT THE TIME OF PROCESSING. RESIDUES -2 TO 0 ARE CLONING ARTIFACTS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rfz.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rfz.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rfz_validation.pdf.gz | 470.2 KB | Display | wwPDB validaton report |
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Full document | 1rfz_full_validation.pdf.gz | 506.1 KB | Display | |
Data in XML | 1rfz_validation.xml.gz | 30 KB | Display | |
Data in CIF | 1rfz_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/1rfz ftp://data.pdbj.org/pub/pdb/validation_reports/rf/1rfz | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-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: 18988.941 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: P84133 #2: Chemical | ChemComp-SO4 / #3: 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: 2.55 Å3/Da / Density % sol: 51.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: ammonium sulfate, BIS-TRIS, pH 5.5, 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-ID / Wavelength: 0.97956, 0.97943, 0.9647 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Feb 6, 2003 / Details: mirrors | ||||||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→47.7 Å / Num. all: 22606 / Num. obs: 22606 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.107 | ||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 15 % / Rmerge(I) obs: 0.792 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→47.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 287184.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.4785 Å2 / ksol: 0.341003 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→47.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.93 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
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Xplor file |
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