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Yorodumi- PDB-2hx8: Crystal structure of Cu(I) Azurin with the metal-binding loop seq... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hx8 | ||||||
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Title | Crystal structure of Cu(I) Azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CSPHQGAGM", at pH5 | ||||||
Components | Azurin | ||||||
Keywords | ELECTRON TRANSPORT / BLUE COPPER-BINDING PROTEIN / GREEK-KEY BETA-BARREL / LOOP MUTAGENESIS | ||||||
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 / Direct use of Oxidised structure in same crystal form / Resolution: 1.6 Å | ||||||
Authors | Banfield, M.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Engineering Copper Sites in Proteins: Loops Confer Native Structures and Properties to Chimeric Cupredoxins. Authors: Li, C. / Banfield, M.J. / Dennison, C. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: Basic requirements for a metal-binding site in a protein: The influence of loop shorteneing on the cupredoxin azurin Authors: Chan, L. / Yanagisawa, S. / Martins, B.M. / Messerschmidt, A. / Banfield, M.J. / Dennison, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hx8.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hx8.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/2hx8 ftp://data.pdbj.org/pub/pdb/validation_reports/hx/2hx8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13785.544 Da / Num. of mol.: 2 / Mutation: Metal binding loop Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu / Plasmid: TRK99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P00282 #2: Chemical | #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: 2.25 Å3/Da / Density % sol: 45.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 29-31% PEG 4000, 100mM magnesium chloride, 100mM Sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 13, 2006 / Details: Osmic "blue" |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.547→54.317 Å / Num. obs: 33470 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.4 / Num. measured all: 31142 / Num. unique all: 4783 / Rsym value: 0.302 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: Direct use of Oxidised structure in same crystal form Starting model: Cu(II) form of the protein Resolution: 1.6→54.31 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.821 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, BUT NOT OUTPUT TO FINAL FILE
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.285 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→54.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.603→1.644 Å / Total num. of bins used: 20
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