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Yorodumi- PDB-4ko6: Investigating the functional significance of the interlocked pair... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ko6 | ||||||
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Title | Investigating the functional significance of the interlocked pair structural determinants in Pseudomonas aeruginosa azurin (V31I/V95K/Y108F) | ||||||
Components | Azurin | ||||||
Keywords | ELECTRON TRANSPORT / cupredoxin fold / computational protein design / copper binding | ||||||
Function / homology | Function and homology information transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.738 Å | ||||||
Authors | Inampudi, K.K. / Meng, W. / Tobin, P.H. / Wilson, C.J. | ||||||
Citation | Journal: To be Published Title: Investigating the functional significance of the interlocked pair structural determinants in Pseudomonas aeruginosa azurin (V31I/V95K/Y108F) Authors: Inampudi, K.K. / Meng, W. / Tobin, P.H. / Wilson, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ko6.cif.gz | 112.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ko6.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ko6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/4ko6 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/4ko6 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 13989.875 Da / Num. of mol.: 4 / Fragment: UNP residues 21-148 / Mutation: V31I/V95K/Y108F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: azu, PA4922 / Production host: Escherichia coli (E. coli) / References: UniProt: P00282 #2: Chemical | ChemComp-CU / #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: 1.99 Å3/Da / Density % sol: 38.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM Tris-HCl, 100 mM lithium nitrate, 10 mM copper sulfate, 30% PEG4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→32.88 Å / Num. obs: 40812 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 |
Reflection shell | Highest resolution: 1.73 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.738→32.874 Å / SU ML: 0.22 / σ(F): 0.02 / Phase error: 27.21 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.738→32.874 Å
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Refine LS restraints |
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LS refinement shell |
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