+Open data
-Basic information
Entry | Database: PDB / ID: 1h1x | ||||||
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Title | Sperm whale Myoglobin mutant T67R S92D | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / GLOBIN / PEROXIDASE / OXYGEN STORAGE / HEME / MUSCLE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Zuccotti, S. / Bolognesi, M. | ||||||
Citation | Journal: Biochem.J. / Year: 2004 Title: Engineering Peroxidase Activity in Myoglobin: The Haem Cavity Structure and Peroxide Activation in the T67R/S92D Mutant and its Derivative Reconstituted with Protohaemin-L-Histidine. Authors: Roncone, R. / Monzani, E. / Murtas, M. / Battaini, G. / Pennati, A. / Sanangelantoni, A.M. / Zuccotti, S. / Bolognesi, M. / Casella, L. #1: Journal: J.Mol.Biol. / Year: 1993 Title: High-Resolution Crystal Structures of Distal Histidine Mutants of Sperm Whale Myoglobin Authors: Quillin, M.L. / Arduini, R.M. / Olson, J.S. / Phillips Jr, G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h1x.cif.gz | 58.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h1x.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 1h1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h1x_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1h1x_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1h1x_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1h1x_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/1h1x ftp://data.pdbj.org/pub/pdb/validation_reports/h1/1h1x | HTTPS FTP |
-Related structure data
Related structure data | 1fcsS 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: 17449.262 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MUTATION THR 67 ARG AND SER 92 ASP / Source: (gene. exp.) PHYSETER CATODON (sperm whale) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-CYN / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Compound details | MEMBER OF THE GLOBIN FAMILY SERVING AS RESERVIOR OF OXYGEN IN MUSCLE CELLS ENGINEERED MUTATION THR ...MEMBER OF THE GLOBIN FAMILY SERVING AS RESERVIOR OF OXYGEN IN MUSCLE CELLS ENGINEERED |
Sequence details | REFERENCE BIOCHIM. BIOPHYS. ACTA 336:318-323(1974) SHOWS CONFLICT AT POSITION 122 OF THE PROTEIN ...REFERENCE BIOCHIM. BIOPHYS. ACTA 336:318-323(1974) SHOWS CONFLICT AT POSITION 122 OF THE PROTEIN SEQUENCE AS INDICATED IN THE DBREF RECORDS BELOW. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 Details: 3M (NH4)2SO4, 5MM K3FE(CN)6, 20MM TRIS/HCL, PH9.0, DROPLET 5:3, RESERVOIR:PROTEIN (43MG/ML), pH 9.00 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Detector: CCD / Date: Apr 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→19 Å / Num. obs: 41560 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 13.51 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 28.97 |
Reflection shell | Resolution: 1.4→1.44 Å / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 3.84 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 19 Å / Redundancy: 13.51 % / Num. measured all: 561360 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 3.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FCS Resolution: 1.4→19 Å / SU B: 1.47 / SU ML: 0.024 / ESU R: 0.044 / ESU R Free: 0.044 Details: C-TERMINAL RESIDUES (Q152, G153) LIE IN A POORLY DEFINED ELECTRON DENSITY REGION.
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Displacement parameters | Biso mean: 16.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→19 Å
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Refinement | *PLUS Rfactor Rfree: 0.15 / Rfactor Rwork: 0.12 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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