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Yorodumi- PDB-1jzg: Pseudomonas aeruginosa Reduced Azurin (Cu1+) Ru(tpy)(phen)(His83) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jzg | ||||||
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Title | Pseudomonas aeruginosa Reduced Azurin (Cu1+) Ru(tpy)(phen)(His83) | ||||||
Components | AZURIN | ||||||
Keywords | ELECTRON TRANSPORT / Reduced Blue-copper / Electron Transfer / Ruthenium | ||||||
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: 1.4 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 | 1jzg.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jzg.ent.gz | 30.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/1jzg ftp://data.pdbj.org/pub/pdb/validation_reports/jz/1jzg | HTTPS FTP |
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-Related structure data
Related structure data | 1jzeC 1jzfSC 1jzhC 1jziC 1jzjC C: citing same article (ref.) S: Starting model for refinement |
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Similar 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-CU1 / |
#3: Chemical | ChemComp-RTB / ( |
#4: Chemical | ChemComp-IMF / |
#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: 2.22 Å3/Da / Density % sol: 44.49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: Si Double / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. all: 24445 / Num. obs: 24445 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.56 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.045 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.4→1.45 Å / Mean I/σ(I) obs: 6.1 / Num. unique all: 2265 / Rsym value: 0.273 / % possible all: 93.2 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.045 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JZF Resolution: 1.4→19.83 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 797515.54 / 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: 23.4081 Å2 / ksol: 0.330759 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→19.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.45 Å / Rfactor Rfree error: 0.024 / 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: 7.9 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.233 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.322 / % reflection Rfree: 8.6 % / Rfactor Rwork: 0.303 |