+Open data
-Basic information
Entry | Database: PDB / ID: 7vqg | ||||||
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Title | The X-ray structure of human neuroglobin A15C mutant | ||||||
Components | Neuroglobin | ||||||
Keywords | OXYGEN BINDING / neuroglobin | ||||||
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 hypoxia / response to hypoxia / mitochondrial matrix ...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 hypoxia / response to hypoxia / mitochondrial matrix / heme binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Lin, Y.W. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: The X-ray structure of human neuroglobin A15C mutant Authors: Lin, Y.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vqg.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vqg.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 7vqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vqg_validation.pdf.gz | 808.2 KB | Display | wwPDB validaton report |
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Full document | 7vqg_full_validation.pdf.gz | 810.6 KB | Display | |
Data in XML | 7vqg_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 7vqg_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/7vqg ftp://data.pdbj.org/pub/pdb/validation_reports/vq/7vqg | HTTPS FTP |
-Related structure data
Related structure data | 1oj6S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16666.076 Da / Num. of mol.: 1 / Mutation: A15C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NGB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPG2 |
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-Non-polymers , 5 types, 163 molecules
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-MES / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% v/v 1,4-Dioxane, 0.1 M MES monohydrate pH 6.5, 1.6 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→36.58 Å / Num. obs: 60134 / % possible obs: 99.66 % / Redundancy: 12.4 % / Biso Wilson estimate: 14.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.012 / Net I/σ(I): 37.83 |
Reflection shell | Resolution: 1.35→1.4 Å / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 10.86 / Num. unique obs: 5676 / CC1/2: 0.994 / Rpim(I) all: 0.151 / % possible all: 96.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OJ6 Resolution: 1.35→36.58 Å / SU ML: 0.092 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.5388 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→36.58 Å
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Refine LS restraints |
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LS refinement shell |
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