+Open data
-Basic information
Entry | Database: PDB / ID: 5ilp | ||||||
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Title | H64Q sperm whale myoglobin with a Fe-tolyl moiety | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / Bioorganometallic / Heme / Myoglobin / Sigma-aryl / Hydrazine / Arylhydrazine / Phenylhydrazine / Iron-carbon / 3-methylphenylhydrazine / meta-tolylhydrazine / 4-chlorophenylhydrazine / para-chlorophenylhydrazine | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Model details | This stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale ...This stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale myoglobin ferric H64A and N-hydroxyamphetamine. | ||||||
Authors | Wang, B. / Thomas, L.M. / Richter-Addo, G.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Inorg. Biochem. / Year: 2016 Title: Organometallic myoglobins: Formation of Fe-carbon bonds and distal pocket effects on aryl ligand conformations. Authors: Wang, B. / Thomas, L.M. / Richter-Addo, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ilp.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ilp.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ilp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/5ilp ftp://data.pdbj.org/pub/pdb/validation_reports/il/5ilp | HTTPS FTP |
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-Related structure data
Related structure data | 5iksC 5ileC 5ilmC 5ilrC 2mbwS C: citing same article (ref.) S: Starting model for refinement |
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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: 17355.145 Da / Num. of mol.: 1 / Mutation: H64Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02185 | ||||||
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#2: Chemical | ChemComp-6CQ / [ | ||||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Sequence details | D123N CONFLICT EXISTS IN UNP ENTRY P02185 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 100 mM Tris-Hcl pH7.4, 1 mM EDTA, 3.0 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 2, 2014 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.88→50 Å / Num. obs: 10620 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.021 / Rrim(I) all: 0.042 / Χ2: 0.806 / Net I/av σ(I): 30.972 / Net I/σ(I): 16.3 / Num. measured all: 39773 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2MBW Resolution: 1.88→33 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.838 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.03 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY ONLY ANISOTROPIC REFINEMENT OF HEME IRON
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.35 Å2 / Biso mean: 20.62 Å2 / Biso min: 8.4 Å2
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Refinement step | Cycle: final / Resolution: 1.88→33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.877→1.926 Å / Total num. of bins used: 20
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