+Open data
-Basic information
Entry | Database: PDB / ID: 1npf | ||||||
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Title | MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITRIC OXIDE | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / HEME / OXYGEN STORAGE / NITRIC OXIDE / MYOGLOBIN / NITROSYL / NO / NITROGEN MONOXIDE / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding ...nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / 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 | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Copeland, D.M. / West, A.H. / Richter-Addo, G.B. | ||||||
Citation | Journal: Proteins / Year: 2003 Title: Crystal structures of ferrous horse heart myoglobin complexed with nitric oxide and nitrosoethane. Authors: Copeland, D.M. / West, A.H. / 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 | 1npf.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1npf.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 1npf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1npf_validation.pdf.gz | 823.6 KB | Display | wwPDB validaton report |
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Full document | 1npf_full_validation.pdf.gz | 827.7 KB | Display | |
Data in XML | 1npf_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 1npf_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1npf ftp://data.pdbj.org/pub/pdb/validation_reports/np/1npf | HTTPS FTP |
-Related structure data
Related structure data | 1npgC 1dwrS 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: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ANIMAL OXYGEN STORAGE / Source: (natural) Equus caballus (horse) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P68082 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-NO / | #5: 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: 1.63 Å3/Da / Density % sol: 23.76 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.4 Details: AMMONIUM SULFATE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Chu, K., (2000) Nature, 403, 921. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 6, 2002 / Details: OSMIC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 17516 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 3.4 / % possible all: 91.1 |
Reflection | *PLUS Num. measured all: 34504 |
Reflection shell | *PLUS % possible obs: 91.1 % / Num. unique obs: 1687 / Num. measured obs: 3332 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DWR Resolution: 1.9→40 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.021 /
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.195 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.384 / Rfactor Rwork: 0.365 |