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Yorodumi- PDB-1dm1: 2.0 A CRYSTAL STRUCTURE OF THE DOUBLE MUTANT H(E7)V, T(E10)R OF M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dm1 | ||||||
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Title | 2.0 A CRYSTAL STRUCTURE OF THE DOUBLE MUTANT H(E7)V, T(E10)R OF MYOGLOBIN FROM APLYSIA LIMACINA | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / GLOBIN FOLD / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / oxidoreductase activity / iron ion binding / heme binding / extracellular region Similarity search - Function | ||||||
Biological species | Aplysia limacina (slug sea hare) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.99 Å | ||||||
Authors | Federici, L. / Savino, C. / Musto, R. / Travaglini-Allocatelli, C. / Cutruzzola, F. / Brunori, M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2000 Title: Engineering His(E7) affects the control of heme reactivity in Aplysia limacina myoglobin. Authors: Federici, L. / Savino, C. / Musto, R. / Travaglini-Allocatelli, C. / Cutruzzola, F. / Brunori, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dm1.cif.gz | 42 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dm1.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dm1_validation.pdf.gz | 466.5 KB | Display | wwPDB validaton report |
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Full document | 1dm1_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | 1dm1_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1dm1_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dm1 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dm1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15322.347 Da / Num. of mol.: 1 / Mutation: V63H, R66T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aplysia limacina (slug sea hare) / Production host: Escherichia coli (E. coli) / References: UniProt: P02210 |
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#2: Chemical | ChemComp-HEM / |
#3: 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: 4.65 Å3/Da / Density % sol: 73.57 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: SODIUM CITRATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 K | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 19, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→59.76 Å / Num. all: 19111 / Biso Wilson estimate: 29.814 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.4 |
Reflection | *PLUS % possible obs: 99.3 % |
-Processing
Software |
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Refinement | Resolution: 1.99→59.76 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.99→59.76 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.215 / Rfactor Rwork: 0.189 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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