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Yorodumi- PDB-6iyh: X-ray sequence and high resolution crystal structure of Persian s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iyh | |||||||||
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Title | X-ray sequence and high resolution crystal structure of Persian sturgeon methemoglobin | |||||||||
Components |
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Keywords | OXYGEN BINDING/TRANSPORT PROTEIN / methemoglobin / heme / iron containing / oxygen-carrying / OXYGEN BINDING-TRANSPORT PROTEIN complex | |||||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Acipenser persicus (Persian sturgeon) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Seyedarabi, A. | |||||||||
Citation | Journal: Biochim Biophys Acta Proteins Proteom / Year: 2019 Title: Novel X-ray sequences and crystal structures of Persian and Starry sturgeon methemoglobins: Highlighting the role of heme pocket waters in causing autoxidation Authors: Seyedarabi, A. / Ariaeenejad, S. / Moosavi-Movahedi, A.A. / Rayati, S. / Poursasan, N. / Asiaie, N. / Seraj, Z. / Mehraban, F. / Seyedarabi, S.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iyh.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iyh.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 6iyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iyh_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6iyh_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6iyh_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 6iyh_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/6iyh ftp://data.pdbj.org/pub/pdb/validation_reports/iy/6iyh | HTTPS FTP |
-Related structure data
Related structure data | 6iyiC 3bomS 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: 15475.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence is derived from structure / Source: (natural) Acipenser persicus (Persian sturgeon) / References: UniProt: A0A1X8XL85*PLUS | ||||
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#2: Protein | Mass: 15752.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence derived from structure / Source: (natural) Acipenser persicus (Persian sturgeon) / References: UniProt: A0A1X8XL86*PLUS | ||||
#3: Chemical | #4: Chemical | ChemComp-PGO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.75 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 and 12%(w/v) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9792 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→52.97 Å / Num. obs: 34936 / % possible obs: 99.98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.7→1.744 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BOM Resolution: 1.7→52.97 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.243 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.094 / 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: 19.137 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→52.97 Å
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Refine LS restraints |
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