+Open data
-Basic information
Entry | Database: PDB / ID: 1npg | ||||||
---|---|---|---|---|---|---|---|
Title | MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITROSOETHANE | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / HEME / OXYGEN STORAGE / NITRIC OXIDE / NITROSOETHANE / MYOGLOBIN / NITROSOALKANE / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1npg.cif.gz | 48.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1npg.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 1npg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1npg_validation.pdf.gz | 820.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1npg_full_validation.pdf.gz | 824.4 KB | Display | |
Data in XML | 1npg_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 1npg_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1npg ftp://data.pdbj.org/pub/pdb/validation_reports/np/1npg | HTTPS FTP |
-Related structure data
Related structure data | 1npfC 1dwrS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-NOE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.56 Å3/Da / Density % sol: 20.38 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 11, 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: 1.7→40 Å / Num. obs: 23424 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.89 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 5.1 / % possible all: 98.2 |
Reflection | *PLUS Num. obs: 13504 / Num. measured all: 39336 |
Reflection shell | *PLUS % possible obs: 98.2 % / Num. unique obs: 1323 / Num. measured obs: 3655 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DWR Resolution: 1.7→40 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.043 Å2 / ksol: 0.349798 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.4 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.022 /
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.198 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.412 / Rfactor Rwork: 0.418 |