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Yorodumi- PDB-6zmy: Crystal structure of hemoglobin from turkey (Meleagiris gallopova... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zmy | |||||||||
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Title | Crystal structure of hemoglobin from turkey (Meleagiris gallopova) crystallized in monoclinic form at 1.66 Angstrom resolution | |||||||||
Components |
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Keywords | OXYGEN STORAGE/OXYGEN TRANSPORT / Hemoglobin / turkey / heme / meleagiris gallopova / monoclinic form / OXYGEN TRANSPORT / OXYGEN STORAGE / OXYGEN STORAGE-OXYGEN TRANSPORT complex | |||||||||
Function / homology | Function and homology information hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Meleagris gallopavo (turkey) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.655 Å | |||||||||
Authors | Pandian, R. / Shobana, N. / Sundaresan, S.S. / Thangaraj, V. / Sayed, Y. / Ponnuswamy, M.N. | |||||||||
Funding support | United Kingdom, Portugal, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Structural studies of hemoglobin from two flightless birds, ostrich and turkey: insights into their differing oxygen-binding properties. Authors: Ramesh, P. / Sundaresan, S.S. / Shobana, N. / Vinuchakkaravarthy, T. / Sivakumar, K. / Yasien, S. / Ponnuswamy, M.N.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zmy.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zmy.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zmy_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6zmy_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6zmy_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 6zmy_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/6zmy ftp://data.pdbj.org/pub/pdb/validation_reports/zm/6zmy | HTTPS FTP |
-Related structure data
Related structure data | 3fs4C 6zmxC 1fawS S: Starting model for refinement C: citing same article (ref.) |
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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: 15334.737 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P81023 #2: Protein | Mass: 16329.866 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P84479, UniProt: G1U9Q8*PLUS #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.3 Å3/Da / Density % sol: 46.44 % / Description: Block |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 50% of PEG3350 in 50mM phosphate buffer at pH7.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.655→64.031 Å / Num. obs: 70052 / % possible obs: 98.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 29.552 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.08 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.655→1.684 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3465 / CC1/2: 0.484 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FAW Resolution: 1.655→64.031 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.05 Å2 / Biso mean: 26.0865 Å2 / Biso min: 6.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.655→64.031 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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