+Open data
-Basic information
Entry | Database: PDB / ID: 1dwt | ||||||
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Title | Photorelaxed horse heart MYOGLOBIN CO complex | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / RESPIRATORY PROTEIN | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Chu, K. / Vojtechovsky, J. / McMahon, B.H. / Sweet, R.M. / Berendzen, J. / Schlichting, I. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Crystal Structure of a New Ligand Binding Intermediate in Wildtype Carbonmonoxy Myoglobin Authors: Chu, K. / Vojtechovsky, J. / Mcmahon, B.H. / Sweet, R.M. / Berendzen, J. / Schlichting, I. #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: Nature / Year: 1994 Title: Crystal Structure of Photolysed Myoglobin Authors: Schlichting, I. / Berendzen, J. / Phillips Jr, G.N. / Sweet, R.M. #3: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dwt.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dwt.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dwt_validation.pdf.gz | 808.9 KB | Display | wwPDB validaton report |
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Full document | 1dwt_full_validation.pdf.gz | 809.3 KB | Display | |
Data in XML | 1dwt_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 1dwt_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/1dwt ftp://data.pdbj.org/pub/pdb/validation_reports/dw/1dwt | HTTPS FTP |
-Related structure data
Related structure data | 1dwrC 1dwsC 1aziS 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 / Source: (natural) Equus caballus (horse) / Organ: HEART / References: UniProt: P68082 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-CMO / | ||
#4: Chemical | #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: 1.8 Å3/Da / Density % sol: 31.66 % Description: THIS DATASET WAS COLLECTED UNDER CONTINUOUS ILLUMIN USING AN AR+ LASER (INTENSITY 4.6 MW/MM^2). PHOTO- RELAXATION WAS ACHIEVED BY ILLUMINATING FOR 6 HOURS AT 160K AND BY SUBSEQUENTLY ...Description: THIS DATASET WAS COLLECTED UNDER CONTINUOUS ILLUMIN USING AN AR+ LASER (INTENSITY 4.6 MW/MM^2). PHOTO- RELAXATION WAS ACHIEVED BY ILLUMINATING FOR 6 HOURS AT 160K AND BY SUBSEQUENTLY RAMPING THE TEMPERATURE TO AT 10K/H, AGAIN UNDER CONTINUOUS ILLUMINATION. AN OX CRYOSTREAM WAS USED FOR TEMPERATURE CONTROL. | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HHMB(SIGMA) WAS CRYSTALLIZED AT ROOM TEMPERATURE BY EQUILIBRATING 10 UL DROPS OF 5 MG/ML PROTEIN IN 1.7-1.8 M AMMONIUM SULFATE, 0.1 M TRIS HCL PH 7.5 USING THE HANGING DROP GEOMETRY | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 88 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.91 |
Detector | Type: BRANDEIS / Detector: CCD / Date: Oct 9, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 23555 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 2.42 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.266 / % possible all: 98 |
Reflection shell | *PLUS % possible obs: 98 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AZI Resolution: 1.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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