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Yorodumi- PDB-7c90: Crystal structure of Cytochrome CL from the marine methylotrophic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c90 | ||||||
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Title | Crystal structure of Cytochrome CL from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT (Ma-CytcL) | ||||||
Components | Cytochrome c, mono-and diheme variant | ||||||
Keywords | ELECTRON TRANSPORT / Methanol Oxidation system / Marine Bacterium / Methylophaga aminisulfidivorans MPT | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Methylophaga aminisulfidivorans MP (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Ghosh, S. / Dhanasingh, I. / Lee, S.H. | ||||||
Citation | Journal: J Microbiol Biotechnol. / Year: 2020 Title: Crystal Structure of CytochromecLfrom the Aquatic Methylotrophic BacteriumMethylophaga aminisulfidivoransMPT. Authors: Ghosh, S. / Dhanasingh, I. / Ryu, J. / Kim, S.W. / Lee, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c90.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c90.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 7c90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/7c90 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/7c90 | HTTPS FTP |
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-Related structure data
Related structure data | 2d0wS 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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 21621.459 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylophaga aminisulfidivorans MP (bacteria) Gene: MAMP_01204 / Production host: Methylophaga aminisulfidivorans (bacteria) / References: UniProt: F5SWR8 |
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-Non-polymers , 7 types, 399 molecules
#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-EPE / #4: Chemical | #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-FE / #7: Chemical | ChemComp-NA / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1600 mM sodium/potassium phosphate monobasic, 100 mM HEPES/sodium hydroxide pH 7.5 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97941 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 21, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97941 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.13→50 Å / Num. obs: 32914 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.042 / Rrim(I) all: 0.111 / Χ2: 2.836 / Net I/σ(I): 11.7 / Num. measured all: 237733 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D0W Resolution: 2.13→30.58 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.622 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 123.04 Å2 / Biso mean: 37.923 Å2 / Biso min: 17.87 Å2
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Refinement step | Cycle: final / Resolution: 2.13→30.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.185 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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