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- PDB-8hm9: X-ray Crystal Structure of Pseudoazurin Met16His Variant at pH 4.0 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hm9 | ||||||
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Title | X-ray Crystal Structure of Pseudoazurin Met16His Variant at pH 4.0 | ||||||
![]() | Pseudoazurin | ||||||
![]() | ELECTRON TRANSPORT / electron transfer protein | ||||||
Function / homology | ![]() electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aoyama, Y. / Yamaguchi, T. / Kohzuma, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray Crystal Structure of Pseudoazurin Met16His Variant at pH 4.0 Authors: Aoyama, Y. / Yamaguchi, T. / Kohzuma, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.6 KB | Display | ![]() |
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PDB format | ![]() | 98.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yl4S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13039.892 Da / Num. of mol.: 2 / Mutation: M16H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 31% PEG1500, 0.1 M potassium phosphate (pH 4.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.052 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→39.77 Å / Num. obs: 47237 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.039 / Rrim(I) all: 0.058 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.36→1.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.267 / Num. unique obs: 2344 / CC1/2: 0.884 / Rpim(I) all: 0.247 / Rrim(I) all: 0.365 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YL4 Resolution: 1.36→39.77 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.37 / SU ML: 0.042 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.051 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.552 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→39.77 Å
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Refine LS restraints |
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LS refinement shell |
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