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- PDB-2qpd: An unexpected outcome of surface-engineering an integral membrane... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qpd | ||||||
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Title | An unexpected outcome of surface-engineering an integral membrane protein: Improved crystallization of cytochrome ba3 oxidase from Thermus thermophilus | ||||||
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![]() | OXIDOREDUCTASE / cytochrome ba3 oxidase / heme / integral membrane protein / Electron transport / Hydrogen ion transport / Ion transport / Iron / Metal-binding / Respiratory chain / Transmembrane / Transport / Formylation | ||||||
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. / Luna, V.M. / Chen, Y. / Stout, C.D. / Fee, J.A. | ||||||
![]() | ![]() Title: An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus. Authors: Liu, B. / Luna, V.M. / Chen, Y. / Stout, C.D. / Fee, J.A. #1: Journal: Protein Expr.Purif. / Year: 2005 Title: A homologous expression system for obtaining engineered cytochrome ba3 from Thermus thermophilus Authors: Chen, Y. / Hunsicker-Wang, L.M. / Pacoma, R.L. / Luna, E. / Fee, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.9 KB | Display | ![]() |
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PDB format | ![]() | 130.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2qpeC ![]() 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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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: 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 , 4 types, 4 molecules ![](data/chem/img/CU1.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.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-CUA / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.34 % |
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Crystal grow | Temperature: 291 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 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2007 / Details: mirrors |
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: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→20 Å / Num. all: 13540 / Num. obs: 13540 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 3.25→3.43 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2076 / % possible all: 82.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XME Resolution: 3.25→19.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.906 / SU B: 48.531 / SU ML: 0.467 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.652 / 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: 44.113 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.087→3.25 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -28.783 Å / Origin y: 22.314 Å / Origin z: -0.518 Å
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Refinement TLS group |
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