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Yorodumi- PDB-4g70: Structure of Recombinant Cytochrome ba3 Oxidase mutant V236T from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g70 | ||||||
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Title | Structure of Recombinant Cytochrome ba3 Oxidase mutant V236T from Thermus thermophilus | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Proton Pump | ||||||
Function / homology | Function and homology information cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / : / copper ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Li, Y. / Chen, Y. / Stout, C.D. | ||||||
Citation | Journal: To be Published Title: Structure of Recombinant Cytochrome ba3 Oxidase mutant V236T from Thermus thermophilus Authors: Li, Y. / Chen, Y. / Stout, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g70.cif.gz | 177.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g70.ent.gz | 136.9 KB | Display | PDB format |
PDBx/mmJSON format | 4g70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g70_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 4g70_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 4g70_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 4g70_validation.cif.gz | 48.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/4g70 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/4g70 | HTTPS FTP |
-Related structure data
Related structure data | |
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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
-Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 63618.211 Da / Num. of mol.: 1 / Mutation: A120F, V236T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: cbaA, TTHA1135 / Plasmid: pmk18 / Production host: Thermus thermophilus (bacteria) / Strain (production host): MT111 / References: UniProt: Q5SJ79, cytochrome-c oxidase |
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#2: Protein | Mass: 18581.299 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: cbaB, ctaC, TTHA1134 / Plasmid: pmk18 / Production host: Thermus thermophilus (bacteria) / Strain (production host): MT111 / References: UniProt: Q5SJ80, cytochrome-c oxidase |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 3769.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: cbaD, TTHA1133 / Plasmid: pmk18 / Production host: Thermus thermophilus (bacteria) / Strain (production host): MT111 / References: UniProt: P82543, cytochrome-c oxidase |
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-Non-polymers , 7 types, 141 molecules
#4: Chemical | ChemComp-HEM / | ||||
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#5: Chemical | ChemComp-HAS / | ||||
#6: Chemical | ChemComp-CU / | ||||
#7: Chemical | ChemComp-PER / | ||||
#8: Chemical | ChemComp-OLC / ( #9: Chemical | ChemComp-CUA / | #10: 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: 3.09 Å3/Da / Density % sol: 60.2 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.5 Details: 50mM Sodium Cacodylate PH 6.5, 1.6M NaCl, 40% PEG400 , Lipidic Cubic Phase, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→75.3 Å / Num. all: 30647 / Num. obs: 30006 / % possible obs: 97.91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→75.3 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.882 / SU B: 9.197 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.533 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.047 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→75.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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