+Open data
-Basic information
Entry | Database: PDB / ID: 3nl7 | ||||||
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Title | Human Hemoglobin A mutant beta H63W carbonmonoxy-form | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / Hemoglobin / ligand migration pathways | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Birukou, I. / Soman, J. / Olson, J.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Blocking the gate to ligand entry in human hemoglobin. Authors: Birukou, I. / Soman, J. / Olson, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nl7.cif.gz | 183.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nl7.ent.gz | 149.6 KB | Display | PDB format |
PDBx/mmJSON format | 3nl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nl7_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3nl7_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3nl7_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 3nl7_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/3nl7 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/3nl7 | HTTPS FTP |
-Related structure data
Related structure data | 3nmlC 3nmmC 3ogbC 2dn3S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P69905 | ||||
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#2: Protein | Mass: 15938.263 Da / Num. of mol.: 1 / Mutation: H63W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P68871 | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.66 % |
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Crystal grow | Temperature: 293 K / Method: small tubes / pH: 6.7 Details: Protein Solution (20mg/ml protein in 0.01 M phosphate pH 7.0) mixed with mother liquor (3.4 M Na/K phosphate, pH6.7) for final concentrations of 2.3 M Na/K phosphate, SMALL TUBES, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 17, 2008 |
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: 1.8→51.27 Å / Num. all: 26616 / Num. obs: 25409 / % possible obs: 95.5 % / Observed criterion σ(I): 3 / Redundancy: 3.74 % / Rmerge(I) obs: 0.074 / Χ2: 0.99 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible obs: 98.8 % / Redundancy: 3.46 % / Rmerge(I) obs: 0.26 / Χ2: 0.99 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2DN3 Resolution: 1.8→31.115 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 22.2 / 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 / Bsol: 53.933 Å2 / ksol: 0.438 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→31.115 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 |
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