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Yorodumi- PDB-1cq2: NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cq2 | ||||||
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Title | NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 ANGSTROM | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / HELICAL / GLOBULAR / ALL-HYDROGEN CONTAINING STRUCTURE / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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 | NEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 2 Å | ||||||
Authors | Shu, F. / Ramakrishnan, V. / Schoenborn, B.P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin. Authors: Shu, F. / Ramakrishnan, V. / Schoenborn, B.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cq2.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cq2.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 1cq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cq2_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 1cq2_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 1cq2_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 1cq2_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/1cq2 ftp://data.pdbj.org/pub/pdb/validation_reports/cq/1cq2 | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 17234.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: PROTEIN IS FULLY DEUTERATED / Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid details: USING T7 EXPRESSION SYSTEM / Plasmid: PET15A / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: SODIUM/POTASSIUM PHOSPHATE, AMMONIUM SULFATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: NUCLEAR REACTOR Type: HIGH FLUX BEAM REACTOR AT BROOKHAVEN NATIONAL LABORATORY Wavelength: 1 |
Detector | Type: MULTI-WIRE DETECTOR FOR NEUTRONS / Detector: AREA DETECTOR / Date: Jan 5, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→62 Å / Num. all: 15372 / Num. obs: 8685 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.158 / % possible all: 92.5 |
Reflection shell | *PLUS % possible obs: 92.5 % |
-Processing
Software |
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Refinement | Resolution: 2→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: USED OMIT MAP TO DETERMINE PROTONATION STATES OF HISTINDINES
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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