+Open data
-Basic information
Entry | Database: PDB / ID: 5yt7 | ||||||
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Title | crystal structure of circularly permutated Azurin 3 | ||||||
Components | Azurin | ||||||
Keywords | METAL BINDING PROTEIN / blue copper protein | ||||||
Function / homology | Function and homology information transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Chen, H.H. / Liu, H.P. / Yu, Y. | ||||||
Citation | Journal: Rsc Adv / Year: 2017 Title: Engineering the Metal-binding Loop of a Blue Copper Protein by Circular Permutation Authors: Chen, H.H. / Su, B. / Zhang, T.T. / Huang, A. / Liu, H.P. / Yu, Y. / Wang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yt7.cif.gz | 230.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yt7.ent.gz | 194.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yt7_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 5yt7_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 5yt7_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 5yt7_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/5yt7 ftp://data.pdbj.org/pub/pdb/validation_reports/yt/5yt7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 14377.308 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: azu, PA4922 / Production host: Escherichia coli (E. coli) / References: UniProt: P00282 |
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-Non-polymers , 6 types, 512 molecules
#2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | ChemComp-NO3 / #5: Chemical | #6: Chemical | #7: 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: 2.37 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.08 M NaOAc, 0.24 M LiNO3, 0.24 M CaCl2, 20% polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→62.02 Å / Num. obs: 62796 / % possible obs: 99.5 % / Redundancy: 7.4 % / Net I/σ(I): 48.4 |
Reflection shell | Resolution: 1.66→1.69 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→62.02 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.016 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.492 Å2
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Refinement step | Cycle: 1 / Resolution: 1.66→62.02 Å
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Refine LS restraints |
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