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- PDB-5l32: Crystal structure of the Zn-RIDC1 complex bearing six interfacial... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l32 | |||||||||
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Title | Crystal structure of the Zn-RIDC1 complex bearing six interfacial disulfide bonds | |||||||||
![]() | Soluble cytochrome b562 | |||||||||
![]() | METAL BINDING PROTEIN / ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Churchfield, L.A. / Tezcan, F.A. | |||||||||
![]() | ![]() Title: De Novo Design of an Allosteric Metalloprotein Assembly with Strained Disulfide Bonds. Authors: Churchfield, L.A. / Medina-Morales, A. / Brodin, J.D. / Perez, A. / 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 | ![]() | 102.9 KB | Display | ![]() |
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PDB format | ![]() | 78.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5l31C ![]() 3hnjS C: citing same article ( 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
#1: Protein | Mass: 11707.218 Da / Num. of mol.: 4 / Fragment: UNP residues 23-128 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HEC / ![]() #3: Chemical | ChemComp-P6G / | ![]() #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.29 % |
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Crystal grow![]() | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris (pH 6.5), 35% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 16, 2013 |
Radiation | Monochromator: Si (111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→37.81 Å / Num. obs: 24815 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.1→2.21 Å / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3HNJ Resolution: 2.1→37.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.419 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.207 / 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: 46.803 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→37.81 Å
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Refine LS restraints |
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