+Open data
-Basic information
Entry | Database: PDB / ID: 5d6m | ||||||
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Title | Mn(II)-loaded MnCcP.1 | ||||||
Components | Cytochrome c peroxidase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Peroxidase fold / Mn(II)-CcP / Mn oxidation / Glutamate | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.653 Å | ||||||
Authors | Robinson, H. / Gao, Y.-G. / Hosseinzadeh, P. / Lu, Y. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Enhancing Mn(II)-Binding and Manganese Peroxidase Activity in a Designed Cytochrome c Peroxidase through Fine-Tuning Secondary-Sphere Interactions. Authors: Hosseinzadeh, P. / Mirts, E.N. / Pfister, T.D. / Gao, Y.G. / Mayne, C. / Robinson, H. / Tajkhorshid, E. / Lu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d6m.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d6m.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 5d6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d6m_validation.pdf.gz | 834.9 KB | Display | wwPDB validaton report |
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Full document | 5d6m_full_validation.pdf.gz | 838.7 KB | Display | |
Data in XML | 5d6m_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 5d6m_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/5d6m ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d6m | HTTPS FTP |
-Related structure data
Related structure data | 2cypS 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: 33260.910 Da / Num. of mol.: 1 / Fragment: UNP residues 71-361 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CCP1, CCP, CPO, YKR066C Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-MN / |
#4: 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: 2.4 Å3/Da / Density % sol: 48.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium iodide, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→41.651 Å / Num. obs: 39151 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.65→1.71 Å / Mean I/σ(I) obs: 5.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CYP Resolution: 1.653→41.651 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 19.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.653→41.651 Å
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Refine LS restraints |
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LS refinement shell |
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