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- PDB-1rkr: CRYSTAL STRUCTURE OF AZURIN-I FROM ALCALIGENES XYLOSOXIDANS NCIMB... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rkr | ||||||
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Title | CRYSTAL STRUCTURE OF AZURIN-I FROM ALCALIGENES XYLOSOXIDANS NCIMB 11015 | ||||||
![]() | AZURIN-I | ||||||
![]() | ELECTRON TRANSPORT | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Li, C. / Inoue, T. / Gotowda, M. / Suzuki, S. / Yamaguchi, K. / Kataoka, K. / Kai, Y. | ||||||
![]() | ![]() Title: Structure of azurin I from the denitrifying bacterium Alcaligenes xylosoxidans NCIMB 11015 at 2.45 A resolution. Authors: Li, C. / Inoue, T. / Gotowda, M. / Suzuki, S. / Yamaguchi, K. / Kunishige, K. / Kai, Y. #1: ![]() Title: Isolation and Characterization of Two Distinct Azurins from Alcaligenes Xylosoxidans Subsp. Xylosoxidans Ncib11015 or Gifu1051 Authors: Yamaguchi, K. / Deligeer / Nakamura, N. / Shidara, S. / Iwasaki, H. / Suzuki, S. #2: ![]() Title: Structure of Azurin from Achromobacter Xylosoxidans Ncib11015 at 2.5 A Resolution Authors: Inoue, T. / Shibata, N. / Nakanishi, H. / Koyama, S. / Ishii, H. / Kai, Y. / Harada, S. / Kasai, N. / Ohshiro, Y. / Suzuki, S. / Kohzuma, T. / Yamaguchi, K. / Shidara, S. / Iwasaki, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.2 KB | Display | ![]() |
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PDB format | ![]() | 84.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13904.841 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-CU / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: HANGING-DROP VAPOR DIFFUSION METHOD, pH 8.0, vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 20, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 11462 / % possible obs: 90.5 % / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.45→2.5 Å / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 3.47 / % possible all: 82.3 |
Reflection | *PLUS Num. measured all: 19618 |
Reflection shell | *PLUS % possible obs: 82.3 % / Num. unique obs: 904 / Num. measured obs: 1087 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: AZURIN-II FROM THE SAME BACTERIUM Resolution: 2.45→8 Å / Data cutoff low absF: 0 / σ(F): 2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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