+Open data
-Basic information
Entry | Database: PDB / ID: 5i28 | ||||||
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Title | Azurin T30R1, crystal form II | ||||||
Components | Azurin | ||||||
Keywords | METAL BINDING PROTEIN / blue copper protein / spin label | ||||||
Function / homology | Function and homology information transition metal ion binding / electron transfer activity / periplasmic space / copper ion binding / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Hagelueken, G. | ||||||
Citation | Journal: Phys Chem Chem Phys / Year: 2016 Title: Determination of nitroxide spin label conformations via PELDOR and X-ray crystallography. Authors: Abdullin, D. / Hagelueken, G. / Schiemann, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i28.cif.gz | 421.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i28.ent.gz | 349.7 KB | Display | PDB format |
PDBx/mmJSON format | 5i28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/5i28 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/5i28 | HTTPS FTP |
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-Related structure data
Related structure data | 5i26C 1e67S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 14148.116 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Gene: azu, PA4922 / Production host: Escherichia coli (E. coli) / References: UniProt: P00282 #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-GOL / | #4: 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: 2.58 Å3/Da / Density % sol: 52.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8943 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→18.22 Å / Num. obs: 166299 / % possible obs: 99.63 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 2.609 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+67 / Resolution: 1.95→18.221 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 34.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→18.221 Å
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Refine LS restraints |
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LS refinement shell |
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