+Open data
-Basic information
Entry | Database: PDB / ID: 5mxz | ||||||
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Title | Kustc0563 Y40F mutant | ||||||
Components | Cytochrome c-552 Ks_3358 | ||||||
Keywords | ELECTRON TRANSPORT / c-type cytochrome / anammox | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Candidatus Kuenenia stuttgartiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Mohd, A. / Barends, T. | ||||||
Citation | Journal: To Be Published Title: Structure and Function of the c-type cytochrome Kustc0563 from Kuenenia stuttgartiensis Authors: Mohd, A. / Barends, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mxz.cif.gz | 37.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mxz.ent.gz | 23.1 KB | Display | PDB format |
PDBx/mmJSON format | 5mxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mxz_validation.pdf.gz | 814.4 KB | Display | wwPDB validaton report |
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Full document | 5mxz_full_validation.pdf.gz | 815 KB | Display | |
Data in XML | 5mxz_validation.xml.gz | 7 KB | Display | |
Data in CIF | 5mxz_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/5mxz ftp://data.pdbj.org/pub/pdb/validation_reports/mx/5mxz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 9502.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Kuenenia stuttgartiensis (bacteria) Gene: kustc0563 / Production host: Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q30JB5 |
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-Non-polymers , 5 types, 79 molecules
#2: Chemical | ChemComp-HEC / | ||||||
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#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ACT / | #6: 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: 2.96 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Zn-acetate, 0.1 M Mes pH 6.0, 10% (w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43 Å / Num. obs: 11201 / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.08 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1627 / CC1/2: 0.86 / Rrim(I) all: 0.854 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: wt structure Resolution: 1.9→42.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.373 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.98 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→42.9 Å
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Refine LS restraints |
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