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Yorodumi- PDB-3zoy: Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zoy | |||||||||
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Title | Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (hexagonal space group) | |||||||||
Components | CYTOCHROME C-552 | |||||||||
Keywords | ELECTRON TRANSPORT / HEMEPROTEIN | |||||||||
Function / homology | Function and homology information periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | NITROSOMONAS EUROPAEA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Hersleth, H.-P. / Can, M. / Krucinska, J. / Zoppellaro, G. / Andersen, N.H. / Wedekind, J.E. / Andersson, K.K. / Bren, K.L. | |||||||||
Citation | Journal: Chembiochem / Year: 2013 Title: Structural Characterization of Nitrosomonas Europaea Cytochrome C-552 Variants with Marked Differences in Electronic Structure. Authors: Can, M. / Krucinska, J. / Zoppellaro, G. / Andersen, N.H. / Wedekind, J.E. / Hersleth, H.-P. / Andersson, K.K. / Bren, K.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zoy.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zoy.ent.gz | 113.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zoy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zoy_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3zoy_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3zoy_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 3zoy_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/3zoy ftp://data.pdbj.org/pub/pdb/validation_reports/zo/3zoy | HTTPS FTP |
-Related structure data
Related structure data | 3zowC 3zoxSC 4jcgC 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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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 8377.599 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) NITROSOMONAS EUROPAEA (bacteria) / Plasmid: PSNEC / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P95339, nitrite reductase (cytochrome; ammonia-forming) #2: Chemical | ChemComp-HEC / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.4 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 0.1 M TRIS-HCL PH 8.5, 3.1 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→68.8 Å / Num. obs: 22416 / % possible obs: 99.5 % / Observed criterion σ(I): 6 / Redundancy: 5.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.7 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZOX Resolution: 2.3→119.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.587 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IT IS COMMON IN PUBLICATIONS ETC. TO START THE NUMBERING OF THE CYTOCHROME C552 NITROSOMONAS EUROPAEA WITH THE FIRST RESIDUE IN THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IT IS COMMON IN PUBLICATIONS ETC. TO START THE NUMBERING OF THE CYTOCHROME C552 NITROSOMONAS EUROPAEA WITH THE FIRST RESIDUE IN THE SEQUENCE BEING NUMBERED AS RESIDUE 3. THEREFORE THE N62DEL MUTANT IS NORMALLY REFERRED TO AS N64DEL. SINGLE-CRYSTAL UV-VIS SPECTRA HAVE BEEN RECORDED BEFORE AND AFTER EXPOSURE TO X-RAYS SHOWING THE RADIATION-INFLUENCE OF THE FERRIC CYTOCHROME C552 CRYSTALS SEE JRNL.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.602 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→119.22 Å
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