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Yorodumi- PDB-3zow: Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zow | ||||||
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Title | Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 | ||||||
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: 2.35 Å | ||||||
Authors | Hersleth, H.-P. / Can, M. / Krucinska, J. / Zoppellaro, G. / Andersen, N.H. / Karlsen, S. / 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 | 3zow.cif.gz | 549.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zow.ent.gz | 465.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zow_validation.pdf.gz | 6.2 MB | Display | wwPDB validaton report |
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Full document | 3zow_full_validation.pdf.gz | 6.2 MB | Display | |
Data in XML | 3zow_validation.xml.gz | 56 KB | Display | |
Data in CIF | 3zow_validation.cif.gz | 78.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/3zow ftp://data.pdbj.org/pub/pdb/validation_reports/zo/3zow | HTTPS FTP |
-Related structure data
Related structure data | 3zoxSC 3zoyC 4jcgC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 8491.702 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) NITROSOMONAS EUROPAEA (bacteria) 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: 2.57 Å3/Da / Density % sol: 51.9 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8496 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 24, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8496 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→38.8 Å / Num. obs: 68939 / % possible obs: 97.1 % / Observed criterion σ(I): 6 / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.2 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZOX Resolution: 2.35→35.22 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.891 / SU B: 13.213 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.382 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. IT IS COMMON IN PUBLICATIONS ETC. TO START THE NUMBERING OF THE CYTOCHROME C552 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 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. 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.493 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→35.22 Å
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