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Yorodumi- PDB-8puq: MetHemoglobin structure from serial synchrotron crystallography w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8puq | ||||||
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Title | MetHemoglobin structure from serial synchrotron crystallography with fixed target | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / Horse hemoglobin / SSX / fixed target | ||||||
Function / homology | Function and homology information hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Bjelcic, M. / Sigfridsson Clauss, K. / Aurelius, O. / Milas, M. / Nan, J. / Ursby, T. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Anaerobic fixed-target serial crystallography using sandwiched silicon nitride membranes. Authors: Bjelcic, M. / Sigfridsson Clauss, K.G.V. / Aurelius, O. / Milas, M. / Nan, J. / Ursby, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8puq.cif.gz | 303.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8puq.ent.gz | 190.5 KB | Display | PDB format |
PDBx/mmJSON format | 8puq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/8puq ftp://data.pdbj.org/pub/pdb/validation_reports/pu/8puq | HTTPS FTP |
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-Related structure data
Related structure data | 8purC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14981.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P01958 | ||||
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#2: Protein | Mass: 16032.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02062 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.34 % |
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Crystal grow | Temperature: 293.15 K / Method: batch mode / pH: 7.5 / Details: 26%v PEG3350, 10mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 293.15 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→53.55 Å / Num. obs: 25258 / % possible obs: 100 % / Redundancy: 176 % / CC1/2: 0.9903 / R split: 0.075 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.95→2.02 Å / Mean I/σ(I) obs: 1.37 / Num. unique obs: 1261 / CC1/2: 0.7593 / R split: 0.4194 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→53.55 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.975 / SU B: 7.71 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.109 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: 63.641 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→53.55 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection: ALL |