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Yorodumi- PDB-5xec: Heterodimer constructed from PA cyt c551-HT cyt c552 and HT cyt c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xec | ||||||||||||
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Title | Heterodimer constructed from PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins | ||||||||||||
Components |
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Keywords | ELECTRON TRANSPORT / Chimeric protein | ||||||||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | ||||||||||||
Biological species | Hydrogenobacter thermophilus (bacteria) Pseudomonas aeruginosa (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||||||||
Authors | Zhang, M. / Nakanishi, T. / Yamanaka, M. / Nagao, S. / Yanagisawa, S. / Shomura, Y. / Shibata, N. / Ogura, T. / Higuchi, Y. / Hirota, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Chembiochem / Year: 2017 Title: Rational Design of Domain-Swapping-Based c-Type Cytochrome Heterodimers by Using Chimeric Proteins. Authors: Zhang, M. / Nakanishi, T. / Yamanaka, M. / Nagao, S. / Yanagisawa, S. / Shomura, Y. / Shibata, N. / Ogura, T. / Higuchi, Y. / Hirota, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xec.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xec.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 5xec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/5xec ftp://data.pdbj.org/pub/pdb/validation_reports/xe/5xec | HTTPS FTP |
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-Related structure data
Related structure data | 5xedC 1ynrS 351cS C: citing same article (ref.) 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
#1: Protein | Mass: 8504.748 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-36,UNP RESIDUES 43-104 Source method: isolated from a genetically manipulated source Details: The chimeric protein of Cytochrome c-552 (19-36) and Cytochrome c-551 (43-104) Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria), (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: DSM 6534 / IAM 12695 / TK-6, ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: HTH_0988, Hydth_0984, nirM, PA0518 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB387 / References: UniProt: P15452, UniProt: P00099 | ||
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#2: Protein | Mass: 8786.158 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 23-42,UNP RESIDUES 37-98 Source method: isolated from a genetically manipulated source Details: The chimeric protein of Cytochrome c-551 (23-42) and Cytochrome c-552 (37-98) Source: (gene. exp.) Pseudomonas aeruginosa (bacteria), (gene. exp.) Hydrogenobacter thermophilus (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1, DSM 6534 / IAM 12695 / TK-6 Gene: nirM, PA0518, HTH_0988, Hydth_0984 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB387 / References: UniProt: P00099, UniProt: P15452 | ||
#3: Chemical | #4: 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: 2.21 Å3/Da / Density % sol: 44.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Tris-HCl containing 200 mM sodium acetate, 30% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 12, 2015 |
Radiation | Monochromator: Fixed exit Si (111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→20 Å / Num. obs: 60431 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8875 / CC1/2: 0.843 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 351C, 1YNR Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.295 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.037 / 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: 12.396 Å2
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Refinement step | Cycle: 1 / Resolution: 1.1→20 Å
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