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- PDB-3qjr: The structure of and photolytic induced changes of carbon monoxid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qjr | ||||||
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Title | The structure of and photolytic induced changes of carbon monoxide binding to the cytochrome ba3-oxidase from Thermus thermophilus | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, B. / Zhang, Y. / Sage, J.T. / Doukov, T. / Chen, Y. / Stout, C.D. / Fee, J.A. | ||||||
![]() | ![]() Title: Structural changes that occur upon photolysis of the Fe(II)(a3)-CO complex in the cytochrome ba(3)-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral ...Title: Structural changes that occur upon photolysis of the Fe(II)(a3)-CO complex in the cytochrome ba(3)-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral study demonstrates CO binding to Cu(B). Authors: Liu, B. / Zhang, Y. / Sage, J.T. / Soltis, S.M. / Doukov, T. / Chen, Y. / Stout, C.D. / Fee, J.A. #1: ![]() 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. #2: ![]() Title: An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba3 from Thermus thermophilus Authors: Liu, B. / Luna, V.M. / Chen, Y. / Stout, C.D. / Fee, J.A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.6 KB | Display | ![]() |
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PDB format | ![]() | 123.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3qjqC ![]() 3qjsC ![]() 3qjtC ![]() 3qjuC ![]() 3qjvC ![]() 1xmeS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB
#1: Protein | ![]() Mass: 63401.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
-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.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 5 molecules ![](data/chem/img/CU1.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/CUA.gif)
#4: Chemical | ChemComp-CU1 / ![]() |
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#5: Chemical | ChemComp-HEM / ![]() |
#6: Chemical | ChemComp-HAS / |
#7: Chemical | ChemComp-CMO / ![]() |
#8: Chemical | ChemComp-CUA / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.66 % |
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Crystal grow![]() | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 7% PEK 2K, 50 mM KCl, 20 mM Bis-Tris pH 7.0, 6.5 mM n-nonyl-beta-D-glucopyranoside , VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 14, 2010 |
Radiation | Monochromator: FLAT MIRROR (VERTICAL FOCUSING), SINGLE CRYSTAL FOCUSING, SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.2→76.94 Å / Num. all: 16200 / Num. obs: 16200 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rsym value: 0.06 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 2339 / Rsym value: 0.385 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1XME Resolution: 3.2→19.89 Å / Cor.coef. Fo:Fc: 0.77 / Cor.coef. Fo:Fc free: 0.76 / SU B: 104.95 / SU ML: 0.707 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.797 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.728 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.281 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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