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Yorodumi- PDB-2hx9: Crystal structure of Cu(I) Azurin with the metal-binding loop seq... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hx9 | ||||||
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Title | Crystal structure of Cu(I) Azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CSPHQGAGM", at pH4 | ||||||
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 / 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 / Direct use of Oxidised structure in same crystal form / Resolution: 1.7 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 | 2hx9.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hx9.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/2hx9 ftp://data.pdbj.org/pub/pdb/validation_reports/hx/2hx9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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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: 2.21 Å3/Da / Density % sol: 44.41 % |
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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. Crystal soaked in pH4 buffer and ascorbate following growth, 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 15, 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: 1.7→54.233 Å / Num. obs: 27616 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.6 / Num. measured all: 19566 / Num. unique all: 3968 / Rsym value: 0.293 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: Direct use of Oxidised structure in same crystal form Resolution: 1.7→33 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.974 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.112 / 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: 18.514 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
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