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Yorodumi- PDB-1dtm: CRYSTAL STRUCTURE OF THE SPERM-WHALE MYOGLOBIN MUTANT H93G COMPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dtm | ||||||
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Title | CRYSTAL STRUCTURE OF THE SPERM-WHALE MYOGLOBIN MUTANT H93G COMPLEXED WITH 4-METHYLIMIDAZOLE, METAQUO FORM | ||||||
Components | RECOMBINANT SPERM WHALE MYOGLOBIN VARIANT H93G | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Heme protein / Myoglobin / ligand-substitution / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.13 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 | 1dtm.cif.gz | 44.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dtm.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dtm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dtm ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dtm | HTTPS FTP |
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-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 Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: PMB413B / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-4MZ / Mass: 82.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N2 Details: 4-methylimidazole from Aldrich Chemical Company (Cat # 19,988-5). 4-methylimidazole substituted for imidazole by extensive buffer exchange using spin-columns equilibrated with 0.1 M 4-methylimidazole. |
#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: 2.26 Å3/Da / Density % sol: 45.69 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 35 % PEG 8000, 0.3-0.35 M NaOAc, 0.1 M PIPES, and 0.1 % dioxane, 0.1 M 4-methylimidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP Temp details: Room temperature | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||
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: Jul 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: 2.13→20 Å / Num. all: 7356 / Num. obs: 7356 / % possible obs: 78.9 % / Redundancy: 2.63 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.54 |
Reflection shell | Resolution: 2.13→2.298 Å / Redundancy: 1.51 % / Rmerge(I) obs: 0.141 / Num. unique all: 853 / % possible all: 49 |
Reflection shell | *PLUS % possible obs: 49 % |
-Processing
Software |
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Refinement | Resolution: 2.13→20 Å Stereochemistry target values: Bond length rmsd 0.02 angstroms, Bond angle 3.0 degrees, B-correlation 6 square angstroms, Trigonal planarity 0.02, Planar groups 0.02 Details: 4-methyl imidazole built into an omit map in the proximal pocket after extensive all-atom refinement of the protein and heme
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Refinement step | Cycle: LAST / Resolution: 2.13→20 Å
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Refine LS restraints |
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