+Open data
-Basic information
Entry | Database: PDB / ID: 1aj9 | ||||||
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Title | R-STATE HUMAN CARBONMONOXYHEMOGLOBIN ALPHA-A53S | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / HEMOGLOBIN / MUTANT / ALPHA-A53S / CARBOXYHEMOGLOBIN / CARBONMONOXIDE / CARBONMONOXYHEMOGLOBIN / CARBONMONOXY | ||||||
Function / homology | Function and homology information nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha 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 / regulation of blood pressure / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / Factors involved in megakaryocyte development and platelet production / tertiary granule lumen / 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: 2.2 Å | ||||||
Authors | Vasquez, G.B. / Ji, X. / Fronticelli, C. / Gilliland, G.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Human carboxyhemoglobin at 2.2 A resolution: structure and solvent comparisons of R-state, R2-state and T-state hemoglobins. Authors: Vasquez, G.B. / Ji, X. / Fronticelli, C. / Gilliland, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aj9.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aj9.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 1aj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aj9_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1aj9_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1aj9_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 1aj9_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/1aj9 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/1aj9 | HTTPS FTP |
-Related structure data
Related structure data | 1hcoS 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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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 15166.353 Da / Num. of mol.: 1 / Mutation: A53S / Source method: isolated from a natural source / Details: OUTDATED BLOOD FROM THE BALTIMORE BLOOD BANK / Source: (natural) Homo sapiens (human) / Cell: ERYTHROCYTE / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P69905 |
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#2: Protein | Mass: 15890.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OUTDATED BLOOD FROM THE BALTIMORE BLOOD BANK / Source: (natural) Homo sapiens (human) / Cell: ERYTHROCYTE / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P68871 |
-Non-polymers , 4 types, 243 molecules
#3: Chemical | ChemComp-PO4 / | ||||
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#4: Chemical | #5: Chemical | #6: 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: 2.23 Å3/Da / Density % sol: 45 % | |||||||||||||||
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Crystal grow | Method: batch method / pH: 6.7 Details: PROTEIN WAS BATCH CRYSTALLIZED IN 2.5 M SODIUM/POTASSIUM PHOSPHATE, PH 6.7, AND 1% (W/V) CARBOXYHEMOGLOBIN., batch method | |||||||||||||||
Crystal grow | *PLUS Method: batch method | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1996 / Details: MONOCHROMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→6 Å / Num. obs: 12412 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.369 / % possible all: 66 |
Reflection | *PLUS Num. measured all: 59019 |
Reflection shell | *PLUS % possible obs: 66 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HCO Resolution: 2.2→6 Å / σ(F): 1
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Displacement parameters | Biso mean: 24.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: GPRLSA / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.155 / Rfactor Rwork: 0.155 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |