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- PDB-3eh5: Structure of the reduced form of cytochrome ba3 oxidase from Ther... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3eh5 | ||||||
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Title | Structure of the reduced form of cytochrome ba3 oxidase from Thermus thermophilus | ||||||
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![]() | OXIDOREDUCTASE / CYTOCHROME BA3 OXIDASE / HEME / INTEGRAL MEMBRANE PROTEIN / COPPER / ELECTRON TRANSPORT / HYDROGEN ION TRANSPORT / ION TRANSPORT / IRON / METAL-BINDING / RESPIRATORY CHAIN / TRANSMEMBRANE / TRANSPORT / FORMYLATION / Cell membrane / Membrane | ||||||
Function / homology | ![]() cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / : / copper ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, B. / Chen, Y. / Doukov, T. / Soltis, S.M. / Stout, D. / Fee, J.A. | ||||||
![]() | ![]() Title: Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the ...Title: Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme. Authors: Liu, B. / Chen, Y. / Doukov, T. / Soltis, S.M. / Stout, C.D. / Fee, J.A. #1: ![]() Title: An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus Authors: Liu, B. / Luna, M. / Chen, Y. / Stout, D. / Fee, J.A. #2: ![]() Title: A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from Thermus thermophilus Authors: Hunsicker-Wang, L.M. / Pacoma, R.L. / Chen, Y. / Fee, J.A. / Stout, C.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.2 KB | Display | ![]() |
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PDB format | ![]() | 134.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 35.5 KB | Display | |
Data in CIF | ![]() | 46.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eh3C ![]() 3eh4C ![]() 1xmeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
-Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 68987.453 Da / Num. of mol.: 1 / Fragment: UNP residues 2-562 / Mutation: K258R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 18349.990 Da / Num. of mol.: 1 / Fragment: UNP residues 3-168 / Mutation: E4Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide / Sugars , 2 types, 5 molecules C![](data/chem/img/BNG.gif)
![](data/chem/img/BNG.gif)
#3: Protein/peptide | Mass: 3638.407 Da / Num. of mol.: 1 / Fragment: UNP residues 2-34 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#7: Sugar | ChemComp-BNG / |
-Non-polymers , 5 types, 87 molecules ![](data/chem/img/CU1.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CU1 / |
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#5: Chemical | ChemComp-HEM / |
#6: Chemical | ChemComp-HAS / |
#8: Chemical | ChemComp-CUA / |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.12 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Peg 2000, Bis-tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC Quantum-315R CCD / Detector: Q315R / Date: Jul 27, 2007 Details: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing). |
Radiation | Monochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. obs: 33534 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.55→2.62 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 0.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XME Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 27.09 / SU ML: 0.286 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.502 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -28.42 Å / Origin y: 22.384 Å / Origin z: -0.441 Å
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Refinement TLS group |
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