[English] 日本語
Yorodumi- PDB-1azi: MYOGLOBIN (HORSE HEART) RECOMBINANT WILD-TYPE COMPLEXED WITH AZIDE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1azi | ||||||
---|---|---|---|---|---|---|---|
Title | MYOGLOBIN (HORSE HEART) RECOMBINANT WILD-TYPE COMPLEXED WITH AZIDE | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / RESPIRATORY PROTEIN | ||||||
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 / Resolution: 2 Å | ||||||
Authors | Maurus, R. / Brayer, G.D. | ||||||
Citation | Journal: Biochem.J. / Year: 1998 Title: Structural and spectroscopic studies of azide complexes of horse heart myoglobin and the His-64-->Thr variant. Authors: Maurus, R. / Bogumil, R. / Nguyen, N.T. / Mauk, A.G. / Brayer, G. #1: Journal: Biochim.Biophys.Acta / Year: 1997 Title: A Myoglobin Variant with a Polar Substitution in a Conserved Hydrophobic Cluster in the Heme Binding Pocket Authors: Maurus, R. / Overall, C.M. / Bogumil, R. / Luo, Y. / Mauk, A.G. / Smith, M. / Brayer, G.D. #2: Journal: J.Biol.Chem. / Year: 1994 Title: Structural Characterization of Heme Ligation in the His64-->Tyr Variant of Myoglobin Authors: Maurus, R. / Bogumil, R. / Luo, Y. / Tang, H.L. / Smith, M. / Mauk, A.G. / Brayer, G.D. #3: Journal: Biochemistry / Year: 1994 Title: Ftir Analysis of the Interaction of Azide with Horse Heart Myoglobin Variants Authors: Bogumil, R. / Hunter, C.L. / Maurus, R. / Tang, H.L. / Lee, H. / Lloyd, E. / Brayer, G.D. / Smith, M. / Mauk, A.G. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Three-Dimensional Structure of Cyanomet-Sulfmyoglobin C Authors: Evans, S.V. / Sishta, B.P. / Mauk, A.G. / Brayer, G.D. #5: Journal: Protein Eng. / Year: 1991 Title: Expression in Escherichia Coli of a Synthetic Gene Coding for Horse Heart Myoglobin Authors: Guillemette, J.G. / Matsushima-Hibiya, Y. / Atkinson, T. / Smith, M. #6: Journal: J.Mol.Biol. / Year: 1990 Title: High-Resolution Study of the Three-Dimensional Structure of Horse Heart Metmyoglobin Authors: Evans, S.V. / Brayer, G.D. #7: Journal: J.Biol.Chem. / Year: 1988 Title: Horse Heart Metmyoglobin. A 2.8-A Resolution Three-Dimensional Structure Determination Authors: Evans, S.V. / Brayer, G.D. #8: Journal: J.Mol.Biol. / Year: 1987 Title: Crystallization and Preliminary Diffraction Data for Horse Heart Metmyoglobin Authors: Sherwood, C. / Mauk, A.G. / Brayer, G.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1azi.cif.gz | 45.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1azi.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 1azi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1azi_validation.pdf.gz | 482.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1azi_full_validation.pdf.gz | 491.7 KB | Display | |
Data in XML | 1azi_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1azi_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/1azi ftp://data.pdbj.org/pub/pdb/validation_reports/az/1azi | HTTPS FTP |
-Related 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 genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Organ: HEART / Production host: Escherichia coli (E. coli) / References: UniProt: P68082 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-AZI / |
#4: Chemical | ChemComp-HEM / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Wavelength: 1.5418 |
---|---|
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 23, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 5531 / % possible obs: 71.8 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.102 |
Reflection | *PLUS Num. measured all: 14776 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→6 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |