+Open data
-Basic information
Entry | Database: PDB / ID: 1ajg | ||||||
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Title | CARBONMONOXY MYOGLOBIN AT 40 K | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / RESPIRATORY PROTEIN / HEME | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.69 Å | ||||||
Authors | Teng, T.Y. / Srajer, V. / Moffat, K. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1994 Title: Photolysis-induced structural changes in single crystals of carbonmonoxy myoglobin at 40 K. Authors: Teng, T.Y. / Srajer, V. / Moffat, K. #1: Journal: Biochemistry / Year: 1997 Title: Initial Trajectory of Carbon Monoxide After Photodissociation from Myoglobin at Cryogenic Temperatures Authors: Teng, T.Y. / Srajer, V. / Moffat, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ajg.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ajg.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ajg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ajg_validation.pdf.gz | 813.1 KB | Display | wwPDB validaton report |
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Full document | 1ajg_full_validation.pdf.gz | 813.4 KB | Display | |
Data in XML | 1ajg_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1ajg_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/1ajg ftp://data.pdbj.org/pub/pdb/validation_reports/aj/1ajg | HTTPS FTP |
-Related structure data
Related structure data | 1ajhC 1mboS 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: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: CARBONMONOXY MYOGLOBIN, CO LIGAND BOUND TO FE OF THE HEME, HEME BOUND TO NE2 OF HIS 93 Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-CMO / | #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: 1.84 Å3/Da / Density % sol: 33.12 % Description: DATA WERE COLLECTED IN DARK USING AN OPEN FLOW NITROGEN/HELIUM CRYOSTAT FOR COOLING. |
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Crystal grow | pH: 6 Details: AS DESCRIBED IN KENDREW,J.C. AND PARRISH,R.G., PROC. ROY. SOC. A (LONDON) 238, 305-324 (1956), pH 6.0 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 40 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.123 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jun 30, 1993 / Details: YES |
Radiation | Monochromator: YES / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.123 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→27.5 Å / Num. obs: 13483 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.69→1.77 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 5.1 / % possible all: 83.5 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1MBO Resolution: 1.69→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2 Details: THE FOLLOWING RESIDUES HAVE BEEN MODELED WITH DISORDERED SIDE CHAINS IN TWO CONFORMERS -- 4 GLU, 21 VAL, 26 GLN, 31 ARG, 61 LEU. IN ADDITION, THE LIGAND CARBONMONOXY WAS REFINED IN SUCH WAY ...Details: THE FOLLOWING RESIDUES HAVE BEEN MODELED WITH DISORDERED SIDE CHAINS IN TWO CONFORMERS -- 4 GLU, 21 VAL, 26 GLN, 31 ARG, 61 LEU. IN ADDITION, THE LIGAND CARBONMONOXY WAS REFINED IN SUCH WAY OF SHARING ELECTRON DENSITY WITH 30% WATER MOLECULE TO SIMULATE THE 30% MET MYOGLOBIN CONTENTS IN THE VERY LAST STAGE OF REFINEMENT.
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Refine analyze | Luzzati coordinate error obs: 0.16 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.77 Å / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.171 / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.29 / Rfactor Rwork: 0.227 |