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Yorodumi- PDB-1rqa: Crystallographic Analysis of the Interaction of Nitric Oxide with... -
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-Basic information
Entry | Database: PDB / ID: 1rqa | ||||||
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Title | Crystallographic Analysis of the Interaction of Nitric Oxide with Quaternary-T Human Hemoglobin. Beta W73E hemoglobin exposed to NO under anaerobic conditions | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / globin / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin 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 / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / 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: 2.11 Å | ||||||
Authors | Chan, N.-L. / Kavanaugh, J.S. / Rogers, P.H. / Arnone, A. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystallographic analysis of the interaction of nitric oxide with quaternary-T human hemoglobin. Authors: Chan, N.-L. / Kavanaugh, J.S. / Rogers, P.H. / Arnone, A. #1: Journal: To be published Title: X-ray Diffraction Studies of Fully Liganded 37beta Mutant Hemoglobins Reveal a T-Like Intermediate Structure with High Ligand Affinity Authors: Kavanaugh, J.S. / Rogers, P.H. / Arnone, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rqa.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rqa.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 1rqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/1rqa ftp://data.pdbj.org/pub/pdb/validation_reports/rq/1rqa | HTTPS FTP |
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-Related 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: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: alpha globin subunits are purified from red blood cells Source: (natural) Homo sapiens (human) / Tissue: blood / References: UniProt: P69905 #2: Protein | Mass: 15865.167 Da / Num. of mol.: 2 / Mutation: W37E, V1M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: Tetramers are reconsituted by combining the mutant beta globin, heme and alpha subunits purified from red blood cells Gene: HBB / Production host: Escherichia coli (E. coli) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-NO / #5: 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: 2.51 Å3/Da / Density % sol: 50.98 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 10 mg/mL human hemoglobin, 10 mM potassium phosphate, 100 mM potassium chloride, 10-12% PEG 6000, 3mM sodium dithionite (under anaerobic conditions), pH 7.0, BATCH METHOD, temperature 298K |
-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: SDMS / Detector: AREA DETECTOR / Date: Sep 23, 1998 |
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: 2.11→55.048 Å / Num. obs: 42912 / % possible obs: 98 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.11→2.27 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 2 / % possible all: 90.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: betaW37E deoxyhemoglobin to be deposited in PDB Resolution: 2.11→10 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.417 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.375 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→10 Å
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