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Yorodumi- PDB-1k1k: Structure of Mutant Human Carbonmonoxyhemoglobin C (beta E6K) at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k1k | ||||||
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Title | Structure of Mutant Human Carbonmonoxyhemoglobin C (beta E6K) at 2.0 Angstrom Resolution in Phosphate Buffer. | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / mutant human hemoglobin C(betaE6K) / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Dewan, J.C. / Taylor-Feeling, A. / Puius, Y.A. / Patskovska, L. / Patskovsky, Y. / Nagel, R.L. / Almo, S.C. / Hirsch, R.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure of mutant human carbonmonoxyhemoglobin C (betaE6K) at 2.0 A resolution. Authors: Dewan, J.C. / Feeling-Taylor, A. / Puius, Y.A. / Patskovska, L. / Patskovsky, Y. / Nagel, R.L. / Almo, S.C. / Hirsch, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k1k.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k1k.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 1k1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k1k_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1k1k_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1k1k_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1k1k_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/1k1k ftp://data.pdbj.org/pub/pdb/validation_reports/k1/1k1k | HTTPS FTP |
-Related structure data
Related structure data | 1hhoS 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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Details | The biological assembly is a tetramer generated from the dimer in the assymetric unit by the two fold axis: -y,-x,1/2-z. |
-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: erythrocyte / Tissue: BLOOD / References: UniProt: P69905 | ||||
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#2: Protein | Mass: 15890.265 Da / Num. of mol.: 1 / Mutation: E6K / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: erythrocyte / Tissue: BLOOD / References: UniProt: P68871 | ||||
#3: Chemical | #4: Chemical | #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: 2.31 Å3/Da / Density % sol: 46.66 % | ||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: batch method / pH: 7.35 Details: potassium phosphate 1.75M, pH 7.35, batch method, temperature 310K | ||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Mar 8, 1995 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→22.55 Å / Num. all: 19382 / Num. obs: 19382 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.38 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 2→2.09 Å / Num. unique all: 2135 / % possible all: 85.16 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 22.5 Å / % possible obs: 94 % / Num. measured all: 84880 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HHO Resolution: 2→22.55 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Details: The side chain of beta K6 was added to the model in weak continuous density present at the 0.5 sigma level in a 2Fo-Fc map.
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Displacement parameters | Biso mean: 24.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→22.55 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 22.5 Å / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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