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- PDB-3hnk: Crystal structure of the dimeric assembly of the cyt cb562 varian... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hnk | ||||||
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Title | Crystal structure of the dimeric assembly of the cyt cb562 variant RIDC-1 | ||||||
![]() | Soluble cytochrome b562 | ||||||
![]() | METAL BINDING PROTEIN / Electron transport | ||||||
Function / homology | ![]() electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Salgado, E.N. / Lewis, R.A. / Brodin, J. / Tezcan, F.A. | ||||||
![]() | ![]() Title: Metal templated design of protein interfaces. Authors: Salgado, E.N. / Ambroggio, X.I. / Brodin, J.D. / Lewis, R.A. / Kuhlman, B. / Tezcan, F.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 | ![]() | 59.4 KB | Display | ![]() |
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PDB format | ![]() | 42.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 3 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106
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Components
#1: Protein | Mass: 11699.084 Da / Num. of mol.: 2 / Mutation: R34A, L38A, Q41W, K42S, D66W, V69I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 26% PEG 2000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: APEX II CCD / Detector: CCD / Date: Oct 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→36.86 Å / Num. all: 12150 / Num. obs: 12085 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1558 / Rsym value: 0.249 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.74 Å2 / Biso mean: 11.957 Å2 / Biso min: 2.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→27.75 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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