+Open data
-Basic information
Entry | Database: PDB / ID: 4mxl | ||||||
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Title | X-ray structure of ZnPFeBMb1 | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / Globin Fold | ||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Chakraborty, S. / Lu, Y. / Petrik, I. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Spectroscopic and computational study of a nonheme iron nitrosyl center in a biosynthetic model of nitric oxide reductase. Authors: Chakraborty, S. / Reed, J. / Ross, M. / Nilges, M.J. / Petrik, I.D. / Ghosh, S. / Hammes-Schiffer, S. / Sage, J.T. / Zhang, Y. / Schulz, C.E. / Lu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mxl.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mxl.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 4mxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mxl_validation.pdf.gz | 834.9 KB | Display | wwPDB validaton report |
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Full document | 4mxl_full_validation.pdf.gz | 839.3 KB | Display | |
Data in XML | 4mxl_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 4mxl_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/4mxl ftp://data.pdbj.org/pub/pdb/validation_reports/mx/4mxl | HTTPS FTP |
-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: 17280.896 Da / Num. of mol.: 1 / Mutation: L29H, F43H, V68E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-ZNH / |
#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: 2.16 Å3/Da / Density % sol: 43.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.77 Details: 0.1M sodium cacodylate, 0.2M NaOAC.3H2O, 30-32% PEG 10K, pH 6.77, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 30, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 24494 / Redundancy: 4.5 % |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.643 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.22 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.074 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30.28 Å
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Refine LS restraints |
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