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Yorodumi- PDB-1jzf: Pseudomonas aeruginosa Oxidized Azurin(Cu2+) Ru(tpy)(phen)(His83) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jzf | ||||||
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Title | Pseudomonas aeruginosa Oxidized Azurin(Cu2+) Ru(tpy)(phen)(His83) | ||||||
Components | AZURIN | ||||||
Keywords | ELECTRON TRANSPORT / Blue-copper / Electron Transfer / Tunneling / Ruthenium / Cu2+ | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Crane, B.R. / Di Bilio, A.J. / Winkler, J.R. / Gray, H.B. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2001 Title: Electron tunneling in single crystals of Pseudomonas aeruginosa azurins. Authors: Crane, B.R. / Di Bilio, A.J. / Winkler, J.R. / Gray, H.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jzf.cif.gz | 39.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jzf.ent.gz | 30.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jzf_validation.pdf.gz | 526.5 KB | Display | wwPDB validaton report |
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Full document | 1jzf_full_validation.pdf.gz | 527.2 KB | Display | |
Data in XML | 1jzf_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 1jzf_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/1jzf ftp://data.pdbj.org/pub/pdb/validation_reports/jz/1jzf | HTTPS FTP |
-Related structure data
-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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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 13961.799 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00282 |
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#2: Chemical | ChemComp-CU / |
#3: Chemical | ChemComp-RTB / ( |
#4: Chemical | ChemComp-IME / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / PH range low: 8 / PH range high: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.03 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 5, 2000 |
Radiation | Monochromator: Double Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 19968 / Num. obs: 19968 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.038 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.5→1.55 Å / Mean I/σ(I) obs: 0.118 / Num. unique all: 1919 / Rsym value: 0.153 / % possible all: 98.9 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 98.9 % / Rmerge(I) obs: 0.038 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→19.78 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 641862.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.9323 Å2 / ksol: 0.352409 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 7.8 % / Rfactor obs: 0.217 / Rfactor Rfree: 0.221 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.259 / % reflection Rfree: 8.5 % / Rfactor Rwork: 0.249 |