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Open data
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Basic information
Entry | Database: PDB / ID: 7kby | ||||||
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Title | Artificial Metalloproteins with Dinuclear Iron Centers | ||||||
![]() | Streptavidin | ||||||
![]() | METAL BINDING PROTEIN / Biotin binding Artificial Metalloprotein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miller, K.R. / Follmer, A.H. / Jasniewski, A.J. / Sabuncu, S. / Biswas, S. / Albert, T. / Hendrich, M.P. / Moenne-Loccoz, P. / Borovik, A.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Artificial Metalloproteins with Dinuclear Iron-Hydroxido Centers. Authors: Miller, K.R. / Biswas, S. / Jasniewski, A. / Follmer, A.H. / Biswas, A. / Albert, T. / Sabuncu, S. / Bominaar, E.L. / Hendrich, M.P. / Moenne-Loccoz, P. / Borovik, A.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44 KB | Display | ![]() |
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PDB format | ![]() | 27.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 726.5 KB | Display | ![]() |
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Full document | ![]() | 728.3 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vo9C ![]() 6vobC ![]() 6vozC ![]() 6vp1C ![]() 6vp2C ![]() 6vp3C ![]() 7kbzC ![]() 7knlC ![]() 2qcbS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16561.932 Da / Num. of mol.: 1 / Mutation: K121A, L124Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-KM3 / { |
#3: Chemical | ChemComp-CYN / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.37 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 26 mg/mL 2.0 M ammonium sulfate, 0.1 M sodium acetate pH 4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→45.86 Å / Num. obs: 17537 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.063 / Rrim(I) all: 0.22 / Net I/σ(I): 9.1 / Num. measured all: 205175 / Scaling rejects: 43 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QCB Resolution: 1.7→41.95 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.81 Å2 / Biso mean: 20.95 Å2 / Biso min: 10.97 Å2
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Refinement step | Cycle: final / Resolution: 1.7→41.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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