+Open data
-Basic information
Entry | Database: PDB / ID: 5ztd | ||||||
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Title | X-ray Crystal Structure of Pseudoazurin Met16Val Variant | ||||||
Components | Pseudoazurin | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Achromobacter cycloclastes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMEN / molecular replacement / Resolution: 1.05 Å | ||||||
Authors | Sakai, C. / Yamaguchi, T. / Kohzuma, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: X-ray Crystal Structure of Pseudoazurin Met16Val Variant Authors: Sakai, C. / Yamaguchi, T. / Kohzuma, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ztd.cif.gz | 183.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ztd.ent.gz | 148 KB | Display | PDB format |
PDBx/mmJSON format | 5ztd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/5ztd ftp://data.pdbj.org/pub/pdb/validation_reports/zt/5ztd | HTTPS FTP |
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-Related structure data
Related structure data | 1bqkS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13000.875 Da / Num. of mol.: 2 / Fragment: UNP residues 29-152 / Mutation: M16V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: bcp / Production host: Escherichia coli (E. coli) / References: UniProt: P19567 #2: Chemical | #3: 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: 2.14 Å3/Da / Density % sol: 42.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Reservoir: 0.1M Tris-HCl (pH 8.5), 27% PEG1000 Drop: 42mg/mL Met16Val Pseudoazurin, 0.1M Tris-HCl (pH 8.5), 13.5% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: Under the cryostream of liquid nitrogen Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 13, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.05→52.365 Å / Num. obs: 93957 / % possible obs: 92.1 % / Redundancy: 7 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.11 / Rsym value: 0.092 / Net I/av σ(I): 4.9 / Net I/σ(I): 11.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.638
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMEN Starting model: 1BQK Resolution: 1.05→24.21 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.05→24.21 Å
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