+Open data
-Basic information
Entry | Database: PDB / ID: 1gbv | ||||||
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Title | (ALPHA-OXY, BETA-(C112G)DEOXY) T-STATE HUMAN HEMOGLOBIN | ||||||
Components | (HEMOGLOBIN) x 2 | ||||||
Keywords | OXYGEN TRANSPORT / HEMOGLOBIN / HUMAN / MUTANT / BETA-C112G / PARTIALLY OXYGENATED / ALPHA-OXY / BETA-DEOXY | ||||||
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 / Resolution: 2 Å | ||||||
Authors | Vasquez, G.B. / Ji, X. / Pechik, I. / Fronticelli, C. / Gilliland, G.L. | ||||||
Citation | Journal: Biophys.J. / Year: 1999 Title: Cysteines beta93 and beta112 as probes of conformational and functional events at the human hemoglobin subunit interfaces. Authors: Vasquez, G.B. / Karavitis, M. / Ji, X. / Pechik, I. / Brinigar, W.S. / Gilliland, G.L. / Fronticelli, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gbv.cif.gz | 132.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gbv.ent.gz | 104.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gbv_validation.pdf.gz | 692.3 KB | Display | wwPDB validaton report |
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Full document | 1gbv_full_validation.pdf.gz | 723.7 KB | Display | |
Data in XML | 1gbv_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1gbv_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/1gbv ftp://data.pdbj.org/pub/pdb/validation_reports/gb/1gbv | HTTPS FTP |
-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 / Mutation: CHAIN B, D, C112G Source method: isolated from a genetically manipulated source Details: ALPHA-OXY, BETA-DEOXY, T STATE / Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD Description: ALPHA CHAINS WERE PURIFIED FROM OUTDATED BLOOD OBTAINED FROM THE BLOOD BANK OF THE UNIVERSITY OF MARYLAND; Cell: ERYTHROCYTE / Organ: BLOOD / Plasmid: PJK05 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905 #2: Protein | Mass: 15844.108 Da / Num. of mol.: 2 / Mutation: CHAIN B, D, C112G Source method: isolated from a genetically manipulated source Details: ALPHA-OXY, BETA-DEOXY, T STATE / Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Description: THE BETA CHAINS WERE RECOMBINANT / Cell: ERYTHROCYTE / Organ: BLOOD / Plasmid: PJK05 / Production host: Escherichia coli (E. coli) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.7 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: unknown / Details: Perutz, M.F., (1968) J. Crystal Growth, 2, 54. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 10, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→6 Å / Num. obs: 34600 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 1.46 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 2.3 |
Reflection | *PLUS % possible obs: 92.8 % / Observed criterion σ(I): 2.3 / Num. measured all: 50688 |
-Processing
Software |
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Refinement | Resolution: 2→6 Å / σ(F): 0
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Displacement parameters | Biso mean: 19.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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