+Open data
-Basic information
Entry | Database: PDB / ID: 1dyz | |||||||||
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Title | OXIDISED AZURIN II FROM ALCALIGENES XYLOSOXIDANS | |||||||||
Components | AZURIN II | |||||||||
Keywords | ELECTRON TRANSPORT / CUPREDOXIN / CUPROPROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | ALCALIGENES XYLOSOXIDANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Dodd, F.E. / Abraham, Z.H.L. / Eady, R.R. / Hasnain, S.S. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structures of Oxidised and Reduced Azurin II from Alcaligenes Xylosoxidans at 1.75 Angstoms Resolution Authors: Dodd, F.E. / Abraham, Z.H.L. / Eady, R.R. / Hasnain, S.S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Structure of a New Azurin from Alcaligenes Xylosoxidans at High Resolution Authors: Dodd, F.E. / Hasnain, S.S. / Abraham, Z.H.L. / Eady, R.R. / Smith, B.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dyz.cif.gz | 38 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dyz.ent.gz | 25 KB | Display | PDB format |
PDBx/mmJSON format | 1dyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dyz_validation.pdf.gz | 412.4 KB | Display | wwPDB validaton report |
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Full document | 1dyz_full_validation.pdf.gz | 412.9 KB | Display | |
Data in XML | 1dyz_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 1dyz_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/1dyz ftp://data.pdbj.org/pub/pdb/validation_reports/dy/1dyz | HTTPS FTP |
-Related structure data
Related structure data | 1dz0C 1arn 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
#1: Protein | Mass: 13793.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCIMB 11015 / Source: (natural) ALCALIGENES XYLOSOXIDANS (bacteria) / Cellular location: PERIPLASM / References: UniProt: P56275 |
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#2: Chemical | ChemComp-CU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 52 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 0.1M KH2 PO4 PH 6.0, 60% SATURATED AMMONIUM SULPHATE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 286 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI BAS-2000 IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 15, 1995 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→37.2 Å / Num. obs: 12084 / % possible obs: 82.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.1 / % possible all: 53.6 |
Reflection | *PLUS Num. measured all: 34438 |
Reflection shell | *PLUS % possible obs: 53.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ARN 1arn Resolution: 1.75→8.5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: DPI = 0.09 ANGSTOMS
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Displacement parameters | Biso mean: 21.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→8.5 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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