+Open data
-Basic information
Entry | Database: PDB / ID: 1a3z | ||||||
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Title | REDUCED RUSTICYANIN AT 1.9 ANGSTROMS | ||||||
Components | RUSTICYANIN | ||||||
Keywords | ELECTRON TRANSPORT / CUPREDOXIN / METALLOPROTEIN / REDOX POTENTIAL / ACIDOPHILIC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acidithiobacillus ferrooxidans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / PHASES TAKEN FROM THE OXIDIZED FORM, PDB ENTRY 1RCY / Resolution: 1.9 Å | ||||||
Authors | Zhao, D. / Shoham, M. | ||||||
Citation | Journal: Biophys.J. / Year: 1998 Title: Rusticyanin: Extremes in acid stability and redox potential explained by the crystal structure. Authors: Zhao, D. / Shoham, M. #1: Journal: J.Mol.Biol. / Year: 1996 Title: Multiple Wavelength Anomalous Diffraction (MAD) Crystal Structure of Rusticyanin: A Highly Oxidizing Cupredoxin with Extreme Acid Stability Authors: Walter, R.L. / Ealick, S.E. / Friedman, A.M. / Blake II, R.C. / Proctor, P. / Shoham, M. #2: Journal: J.Mol.Biol. / Year: 1996 Title: NMR Solution Structure of Cu(I) Rusticyanin from Thiobacillus Ferrooxidans: Structural Basis for the Extreme Acid Stability and Redox Potential Authors: Botuyan, M.V. / Toy-Palmer, A. / Chung, J. / Blake II, R.C. / Beroza, P. / Case, D.A. / Dyson, H.J. #3: Journal: J.Mol.Biol. / Year: 1992 Title: Crystallization and Preliminary X-Ray Crystallographic Studies of Rusticyanin from Thiobacillus Ferrooxidans Authors: Djebli, A. / Proctor, P. / Blake II, R.C. / Shoham, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a3z.cif.gz | 42.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a3z.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 1a3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3z ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3z | HTTPS FTP |
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-Related structure data
Related structure data | 1rcyS 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
#1: Protein | Mass: 16569.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: REDUCED FORM / Source: (natural) Acidithiobacillus ferrooxidans (bacteria) / Cellular location: PERIPLASM / References: UniProt: P24930, UniProt: P0C918*PLUS |
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#2: Chemical | ChemComp-CU1 / |
#3: 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 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.6 Details: VAPOR DIFFUSION IN HANGING DROPS AGAINST 100 MM-SODIUM CITRATE, PH 4.6, 200 MM LITHIUM CHLORIDE AND 25%(W/V) PEG 8000 AT 277K. CRYSTALS SOAKED IN 10MM DITHIONITE FOR 3 DAYS PRIOR TO DATA ...Details: VAPOR DIFFUSION IN HANGING DROPS AGAINST 100 MM-SODIUM CITRATE, PH 4.6, 200 MM LITHIUM CHLORIDE AND 25%(W/V) PEG 8000 AT 277K. CRYSTALS SOAKED IN 10MM DITHIONITE FOR 3 DAYS PRIOR TO DATA COLLECTION., vapor diffusion - hanging drop |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: ADSC / Detector: AREA DETECTOR / Date: Jun 1, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. obs: 9718 / % possible obs: 87.4 % / Observed criterion σ(I): 0 / Redundancy: 1.97 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.9→1.969 Å / Redundancy: 1.42 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 3.02 / Rsym value: 0.199 / % possible all: 78 |
-Processing
Software |
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Refinement | Method to determine structure: PHASES TAKEN FROM THE OXIDIZED FORM, PDB ENTRY 1RCY Starting model: PDB ENTRY 1RCY Resolution: 1.9→100 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Xplor file |
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