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Yorodumi- PDB-1r1c: PSEUDOMONAS AERUGINOSA W48F/Y72F/H83Q/Y108W-AZURIN RE(PHEN)(CO)3(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r1c | ||||||
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Title | PSEUDOMONAS AERUGINOSA W48F/Y72F/H83Q/Y108W-AZURIN RE(PHEN)(CO)3(HIS107) | ||||||
Components | Azurin | ||||||
Keywords | ELECTRON TRANSPORT / BLUE-COPPER / ELECTRON-TRANSFER / RHENIUM / TUNNELING / RADICAL / EPR | ||||||
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: 1.9 Å | ||||||
Authors | Miller, J.E. / Gradinaru, C. / Crane, B.R. / Di Bilio, A.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2003 Title: Spectroscopy and reactivity of a photogenerated tryptophan radical in a structurally defined protein environment Authors: Miller, J.E. / Gradinaru, C. / Crane, B.R. / Di Bilio, A.J. / Wehbi, W.A. / Un, S. / 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 | 1r1c.cif.gz | 123.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r1c.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 1r1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/1r1c ftp://data.pdbj.org/pub/pdb/validation_reports/r1/1r1c | HTTPS FTP |
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-Related structure data
Related structure data | 1bexS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 13929.798 Da / Num. of mol.: 4 / Mutation: W48F/Y72F/H83Q/Q107H/Y108W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: AZU OR PA4922 / Plasmid: PET9A(ASA) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00282 #2: Chemical | ChemComp-CU1 / #3: Chemical | ChemComp-REP / ( #4: 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: 1.95 Å3/Da / Density % sol: 46.59 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 4000, lithium nitrate, imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
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: CHESS / Beamline: F2 / Wavelength: 0.964 / Wavelength: 0.964 Å | |||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 8, 2002 | |||||||||
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→40 Å / Num. obs: 76883 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rsym value: 0.075 / Net I/σ(I): 14 | |||||||||
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.61 % / Mean I/σ(I) obs: 3.35 / Rsym value: 0.374 / % possible all: 97.8 | |||||||||
Reflection | *PLUS Highest resolution: 1.9 Å / Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BEX Resolution: 1.9→40 Å / Num. parameters: 17719 / Num. restraintsaints: 16833 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28(1995)53-56.
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Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4279 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2 Å /
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Refinement | *PLUS Highest resolution: 1.9 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.224 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |