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- PDB-3bvd: Structure of Surface-engineered Cytochrome ba3 Oxidase from Therm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bvd | ||||||
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Title | Structure of Surface-engineered Cytochrome ba3 Oxidase from Thermus thermophilus under Xenon Pressure, 100psi 5min | ||||||
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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 / XENON | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Luna, V.M. / Chen, Y. / Fee, J.A. / Stout, C.D. | ||||||
![]() | ![]() Title: Crystallographic Studies of Xe and Kr Binding within the Large Internal Cavity of Cytochrome ba3 from Thermus thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme-Cu Oxidases. Authors: Luna, V.M. / Chen, Y. / Fee, J.A. / Stout, C.D. #1: ![]() 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. #2: ![]() Title: A novel cryoprotection scheme for enchancing 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 | ![]() | 146.8 KB | Display | ![]() |
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PDB format | ![]() | 109.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1xmeS 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: 63430.008 Da / Num. of mol.: 1 / Mutation: K258R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 18580.314 Da / Num. of mol.: 1 / Mutation: E4Q 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, 11 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/CUA.gif)
#4: Chemical | ChemComp-CU / | ||
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#5: Chemical | ChemComp-HEM / | ||
#6: Chemical | ChemComp-HAS / | ||
#7: Chemical | ChemComp-XE / #8: Chemical | ChemComp-CUA / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.65 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion / pH: 7 Details: 6-9% PEG 2000, 50mM KCl, 7.5-30mM bis-Tris pH 7.0, 6.5mM nonyl-B-D-glucopyranoside , VAPOR DIFFUSION, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2007 Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: Side-scattering cuberoot I-beam bent single crystal; asymmetric cut 12.2 degs. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.37→27.16 Å / Num. all: 16390 / Num. obs: 16341 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 108.222 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 3.37→3.55 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2339 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XME Resolution: 3.37→26.96 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.826 / SU B: 38.25 / SU ML: 0.624 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.712 / 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: 85.48 Å2
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Refinement step | Cycle: LAST / Resolution: 3.37→26.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.37→3.58 Å / Total num. of bins used: 20
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