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Yorodumi- PDB-4f6f: Carbonmonoxy structure of His100Phe Cerebratulus lacteus mini-hem... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f6f | ||||||
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Title | Carbonmonoxy structure of His100Phe Cerebratulus lacteus mini-hemoglobin | ||||||
Components | Neural hemoglobin | ||||||
Keywords | OXYGEN TRANSPORT / oxygen-storage / apolar tunnel | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Cerebratulus lacteus (milky ribbon-worm) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.56 Å | ||||||
Authors | Soman, J. / Salter, M.D. / Olson, J.S. | ||||||
Citation | Journal: To be Published Title: Carbonmonoxy structure of His100Phe Cerebratulus lacteus mini-hemoglobin Authors: Soman, J. / Salter, M.D. / Olson, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f6f.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f6f.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 4f6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/4f6f ftp://data.pdbj.org/pub/pdb/validation_reports/f6/4f6f | HTTPS FTP |
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-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: 11555.977 Da / Num. of mol.: 1 / Mutation: His100Phe Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cerebratulus lacteus (milky ribbon-worm) Production host: Escherichia coli (E. coli) / References: UniProt: O76242 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-CMO / |
#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: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: Protein crystallized from 2.5 mM Ammonium Sulfate and 0.1M sodium Citrate , pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5412 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5412 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.56→27.04 Å / Num. obs: 14611 / % possible obs: 90 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.046 / Χ2: 0.98 / Net I/σ(I): 15.2 / Scaling rejects: 355 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.56→27.04 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8573 / SU ML: 0.24 / σ(F): 1.38 / Phase error: 20.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.471 Å2 / ksol: 0.409 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.11 Å2 / Biso mean: 16.8625 Å2 / Biso min: 7.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→27.04 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 30.7526 Å / Origin y: 35.886 Å / Origin z: 10.5699 Å
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Refinement TLS group |
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