+Open data
-Basic information
Entry | Database: PDB / ID: 1a00 | ||||||
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Title | HEMOGLOBIN (VAL BETA1 MET, TRP BETA37 TYR) MUTANT | ||||||
Components |
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Keywords | OXYGEN TRANSPORT | ||||||
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 / ISOMORPHOUS WITH DEOXYHEMOGLOBIN A / Resolution: 2 Å | ||||||
Authors | Kavanaugh, J.S. / Arnone, A. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: High-resolution crystal structures of human hemoglobin with mutations at tryptophan 37beta: structural basis for a high-affinity T-state,. Authors: Kavanaugh, J.S. / Weydert, J.A. / Rogers, P.H. / Arnone, A. #1: Journal: Biochemistry / Year: 1992 Title: High-Resolution X-Ray Study of Deoxyhemoglobin Rothschild 37 Beta Trp-->Arg: A Mutation that Creates an Intersubunit Chloride-Binding Site Authors: Kavanaugh, J.S. / Rogers, P.H. / Case, D.A. / Arnone, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a00.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a00.ent.gz | 101.9 KB | Display | PDB format |
PDBx/mmJSON format | 1a00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a00_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1a00_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1a00_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 1a00_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a00 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a00 | HTTPS FTP |
-Related structure data
Related structure data | 1a01C 1a0uC 1a0zSC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.95067, -0.05056, 0.30605), Vector: |
-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Gene: HUMAN BETA GLOBIN / Organ: BLOOD / Gene (production host): HUMAN BETA GLOBIN / Production host: Escherichia coli (E. coli) / References: UniProt: P69905 #2: Protein | Mass: 15899.228 Da / Num. of mol.: 2 / Mutation: V1M, W37Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Gene: HUMAN BETA GLOBIN / Organ: BLOOD / Gene (production host): HUMAN BETA GLOBIN / Production host: Escherichia coli (E. coli) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: 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: 2.32 Å3/Da / Density % sol: 47 % Description: BV1M STRUCTURE IN ENTRY 1A0Z WAS USED AS THE STARTING MODEL FOR RIGID BODY REFINEMENT WITH X-PLOR FOLLOWED BY LEAST-SQUARES REFINEMENT WITH PROLSQ. | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 10.5% PEG 6000 10 MM POTASSIUM PHOSPHATE PH 7.0 100 MM POTASSIUM CHLORIDE 3 MM SODIUM DITHIONITE | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 31, 1995 |
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→25 Å / Num. obs: 40226 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 3 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 2.24 / Rsym value: 0.191 / % possible all: 86.3 |
Reflection | *PLUS Num. measured all: 237463 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH DEOXYHEMOGLOBIN A Starting model: BV1M STRUCTURE, PDB ENTRY 1A0Z. Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: THE STARTING MODEL FOR REFINEMENT WAS THE BV1M STRUCTURE IN PDB ENTRY 1A0Z.
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Displacement parameters | Biso mean: 21.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |