+Open data
-Basic information
Entry | Database: PDB / ID: 6h6j | ||||||
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Title | Carbomonoxy murine neuroglobin Gly-loop mutant | ||||||
Components | Neuroglobin | ||||||
Keywords | OXYGEN BINDING / heme protein / gas sensing | ||||||
Function / homology | Function and homology information Intracellular oxygen transport / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hydrogen peroxide / neuron projection development / cellular response to hypoxia ...Intracellular oxygen transport / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hydrogen peroxide / neuron projection development / cellular response to hypoxia / perikaryon / response to hypoxia / mitochondrial matrix / heme binding / negative regulation of apoptotic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Exertier, C. / Vallone, B. / Savino, C. / Freda, I. / Montemiglio, L.C. / Cerutti, G. / Scaglione, A. / Parisi, G. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Sci Rep / Year: 2019 Title: Proximal and distal control for ligand binding in neuroglobin: role of the CD loop and evidence for His64 gating. Authors: Exertier, C. / Milazzo, L. / Freda, I. / Montemiglio, L.C. / Scaglione, A. / Cerutti, G. / Parisi, G. / Anselmi, M. / Smulevich, G. / Savino, C. / Vallone, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h6j.cif.gz | 51 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h6j.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 6h6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h6j_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6h6j_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6h6j_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 6h6j_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/6h6j ftp://data.pdbj.org/pub/pdb/validation_reports/h6/6h6j | HTTPS FTP |
-Related structure data
Related structure data | 6h5zC 6h6cC 6h6iC 1w92S S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16712.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9ER97 |
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-Non-polymers , 7 types, 63 molecules
#2: Chemical | ChemComp-HEM / | ||||||||
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#3: Chemical | ChemComp-CMO / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Chemical | #7: Chemical | #8: 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: 3.61 Å3/Da / Density % sol: 65.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6 M ammonium sulfate, 0.1 M tris pH 7.5, 4% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→38.6 Å / Num. obs: 7550 / % possible obs: 90.4 % / Redundancy: 6 % / CC1/2: 0.9 / Rmerge(I) obs: 0.194 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 2.6→2.75 Å / Num. unique all: 2443 / CC1/2: 0.104 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1W92 Resolution: 2.6→38.64 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.484 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 42.223 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→38.64 Å
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Refine LS restraints |
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