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Yorodumi- PDB-5nc0: The 0.91 A resolution structure of the L16G mutant of cytochrome ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nc0 | |||||||||
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Title | The 0.91 A resolution structure of the L16G mutant of cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitric oxide | |||||||||
Components | Cytochrome c' | |||||||||
Keywords | OXIDOREDUCTASE / nitric oxide / cytochrome / homodimer | |||||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Alcaligenes xylosoxydans xylosoxydans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.91 Å | |||||||||
Authors | Strange, R. / Hough, M. / Antonyuk, S. / Rustage, N. | |||||||||
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 | 5nc0.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nc0.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 5nc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nc0_validation.pdf.gz | 817.1 KB | Display | wwPDB validaton report |
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Full document | 5nc0_full_validation.pdf.gz | 817.3 KB | Display | |
Data in XML | 5nc0_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 5nc0_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/5nc0 ftp://data.pdbj.org/pub/pdb/validation_reports/nc/5nc0 | HTTPS FTP |
-Related structure data
Related structure data | 5ngxC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13575.336 Da / Num. of mol.: 1 / Mutation: L16G Source method: isolated from a genetically manipulated source Details: residue PCA is pyroglutamic acid - 2-pyrrolidone-5-carboxylic acid Source: (gene. exp.) Alcaligenes xylosoxydans xylosoxydans (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: P00138 |
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-Non-polymers , 7 types, 242 molecules
#2: Chemical | ChemComp-HEC / | ||||||
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#3: Chemical | ChemComp-NO / | ||||||
#4: Chemical | ChemComp-NO3 / | ||||||
#5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | #8: 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: 2.67 Å3/Da / Density % sol: 53.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: AMMONIUM SULPHATE, TRIS PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.7872 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7872 Å / Relative weight: 1 |
Reflection | Resolution: 0.91→44.07 Å / Num. obs: 106845 / % possible obs: 99.5 % / Redundancy: 8 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 0.91→0.93 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4889 / CC1/2: 0.547 / Rpim(I) all: 0.564 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YL7 Resolution: 0.91→44.07 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.378 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.014 / 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: 8.977 Å2
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Refinement step | Cycle: 1 / Resolution: 0.91→44.07 Å
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Refine LS restraints |
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