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Yorodumi- PDB-5ngx: The 1.06 A resolution structure of the L16G mutant of ferric cyto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ngx | |||||||||
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Title | The 1.06 A resolution structure of the L16G mutant of ferric cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitrite | |||||||||
Components | Cytochrome c' | |||||||||
Keywords | OXIDOREDUCTASE / nitrite / cytochrome / homodimer / ferric / heme | |||||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Alcaligenes xylosoxydans xylosoxydans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å | |||||||||
Authors | Strange, R. / Hough, M. / Kekelli, D. / Horrell, S. / Moreno Chicano, T. | |||||||||
Citation | Journal: Inorg.Chem. / Year: 2017 Title: Distinguishing Nitro vs Nitrito Coordination in Cytochrome c' Using Vibrational Spectroscopy and Density Functional Theory. Authors: Nilsson, Z.N. / Mandella, B.L. / Sen, K. / Kekilli, D. / Hough, M.A. / Moenne-Loccoz, P. / Strange, R.W. / Andrew, C.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ngx.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ngx.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ngx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/5ngx ftp://data.pdbj.org/pub/pdb/validation_reports/ng/5ngx | HTTPS FTP |
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-Related structure data
Related structure data | 5nc0C 2yl7S S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13446.155 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes xylosoxydans xylosoxydans (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: P00138 |
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#2: Chemical | ChemComp-HEC / |
#3: Chemical | ChemComp-NO2 / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.86 Å3/Da / Density % sol: 56.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM sodium nitrite, 2.2 M ammonium sulphate and 0.1 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→45.24 Å / Num. obs: 70168 / % possible obs: 96.8 % / Redundancy: 7.7 % / Biso Wilson estimate: 8.53 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.023 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.06→1.08 Å / Redundancy: 5.1 % / Num. unique obs: 3511 / CC1/2: 0.587 / Rpim(I) all: 0.493 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2yl7 Resolution: 1.06→45.24 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.121 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 14.673 Å2
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Refinement step | Cycle: 1 / Resolution: 1.06→45.24 Å
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Refine LS restraints |
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