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Yorodumi- PDB-1duo: SPERM WHALE METAQUOMYOGLOBIN PROXIMAL HISTIDINE MUTANT H93G WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1duo | |||||||||
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Title | SPERM WHALE METAQUOMYOGLOBIN PROXIMAL HISTIDINE MUTANT H93G WITH 1-METHYLIMIDAZOLE AS PROXIMAL LIGAND. | |||||||||
Components | SPERM WHALE METAQUOMYOGLOBIN VARIANT H93G | |||||||||
Keywords | OXIDOREDUCTASE / Myoglobin / ligand substitution / heme protein | |||||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | |||||||||
Biological species | Physeter catodon (sperm whale) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Barrick, D. / Dahlquist, F.W. | |||||||||
Citation | Journal: Proteins / Year: 2000 Title: Trans-substitution of the proximal hydrogen bond in myoglobin: I. Structural consequences of hydrogen bond deletion. Authors: Barrick, D. / Dahlquist, F.W. #1: Journal: To be Published Title: Trans-substitution of the proximal hydrogen bond in myoglobin: II. Energetics, functional consequences, and implications for hemoglobin allostery. Authors: Barrick, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1duo.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1duo.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 1duo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1duo_validation.pdf.gz | 825.6 KB | Display | wwPDB validaton report |
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Full document | 1duo_full_validation.pdf.gz | 833.6 KB | Display | |
Data in XML | 1duo_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 1duo_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/1duo ftp://data.pdbj.org/pub/pdb/validation_reports/du/1duo | 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: 17153.857 Da / Num. of mol.: 1 / Mutation: H93G Source method: isolated from a genetically manipulated source Details: HEME IS BOUND TO THE PROTEIN DURING BACTERIAL EXPRESSION Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: P413B / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-1MZ / |
#4: 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: 2.27 Å3/Da / Density % sol: 45.9 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 35 % PEG 8000, 0.3 M NaOAc, 0.1 M PIPES, and 0.1 % dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP Temp details: Room temperature | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Nov 29, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 9290 / Num. obs: 9290 / % possible obs: 76 % / Redundancy: 2.19 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 1.36 % / Rmerge(I) obs: 0.182 / Num. unique all: 1522 / % possible all: 71.1 |
Reflection shell | *PLUS % possible obs: 71.1 % |
-Processing
Software |
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Refinement | Resolution: 2→20 Å Stereochemistry target values: Bond length 0.02 angstroms; Bond angles 3 degrees; Trig planes 0.02, General planes 0.02; B-correlation 6.0 angstroms squared.
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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