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- PDB-4ney: Crystal Structure of an engineered protein with ferredoxin fold, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ney | ||||||
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Title | Crystal Structure of an engineered protein with ferredoxin fold, Northeast Structural Genomics Consortium (NESG) Target OR277 | ||||||
![]() | Engineered protein OR277![]() | ||||||
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Function / homology | ![]() ![]() | ||||||
Biological species | artificial gene (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guan, R. / Lin, Y.-R. / Koga, N. / Koga, R. / Castellanos, J. / Seetharaman, J. / Maglaqui, M. / Sahdev, S. / Mao, L. / Xiao, R. ...Guan, R. / Lin, Y.-R. / Koga, N. / Koga, R. / Castellanos, J. / Seetharaman, J. / Maglaqui, M. / Sahdev, S. / Mao, L. / Xiao, R. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Northeast Structural Genomics Consortium Target OR277 Authors: Guan, R. / Lin, Y.-R. / Koga, N. / Koga, R. / Castellanos, J. / Seetharaman, J. / Maglaqui, M. / Sahdev, S. / Mao, L. / Xiao, R. / Everett, J.K. / Baker, D. / Montelione, G.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.9 KB | Display | ![]() |
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PDB format | ![]() | 128.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | dimer,39.48 kD,98.5% |
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Components
#1: Protein | ![]() Mass: 20456.123 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This is a designed protein. / Source: (synth.) artificial gene (others) #2: Chemical | ChemComp-TRS / | ![]() #3: Chemical | ChemComp-4NE / | #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Protein solution - 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution - 25% PEG 3350, 5% w/v Tetrabutylphosphonium bromide, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 28, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.32→50 Å / Num. all: 15080 / Num. obs: 15080 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Biso Wilson estimate: 38.82 Å2 / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 2.32→2.36 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 7.08 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.323→39.645 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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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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