+Open data
-Basic information
Entry | Database: PDB / ID: 5eet | ||||||
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Title | Crystal structure of murine neuroglobin at ambient pressure | ||||||
Components | Neuroglobin | ||||||
Keywords | TRANSPORT PROTEIN / GLOBIN / OXYGEN STORAGE-TRANSPORTER / HPMX | ||||||
Function / homology | Function and homology information Intracellular oxygen transport / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / 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 / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / 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 / molecular replacement / Resolution: 2 Å | ||||||
Authors | Colloc'h, N. / Girard, E. / Vallone, B. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography. Authors: Colloc'h, N. / Sacquin-Mora, S. / Avella, G. / Dhaussy, A.C. / Prange, T. / Vallone, B. / Girard, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eet.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eet.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 5eet.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eet_validation.pdf.gz | 396.7 KB | Display | wwPDB validaton report |
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Full document | 5eet_full_validation.pdf.gz | 397.1 KB | Display | |
Data in XML | 5eet_validation.xml.gz | 9 KB | Display | |
Data in CIF | 5eet_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/5eet ftp://data.pdbj.org/pub/pdb/validation_reports/ee/5eet | HTTPS FTP |
-Related structure data
Related structure data | 5eohC 5eqmC 5eu2C 5ev5C 5eyjC 5eysC 5f0bC 5f2aC 4o4tS 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
#1: Protein | Mass: 16634.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PlysS / References: UniProt: Q9ER97 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-SO4 / |
#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: 2.58 Å3/Da / Density % sol: 52.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M ammonium sulfate, 0.1 M MES, 10 % dioxane |
-Data collection
Diffraction | Mean temperature: 293 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: CRISTAL / Wavelength: 0.454 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 2, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.454 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4 % / Number: 47048 / Rsym value: 0.104 / D res high: 2 Å / D res low: 45.821 Å / Num. obs: 11623 / % possible obs: 98.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2→45.821 Å / Num. all: 11623 / Num. obs: 11623 / % possible obs: 98.7 % / Redundancy: 4 % / Rpim(I) all: 0.056 / Rrim(I) all: 0.119 / Rsym value: 0.104 / Net I/av σ(I): 5.818 / Net I/σ(I): 10.2 / Num. measured all: 47048 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 11623 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O4T Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1758 / WRfactor Rwork: 0.1375 / FOM work R set: 0.8787 / SU B: 3.571 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1425 / SU Rfree: 0.1288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 103.21 Å2 / Biso mean: 29.779 Å2 / Biso min: 9.64 Å2
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Refinement step | Cycle: final / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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