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- PDB-4jea: Crystal structure of an engineered Zn-RIDC1 construct with four i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jea | ||||||
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Title | Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide bonds | ||||||
![]() | soluble cytochrome b562 | ||||||
![]() | ELECTRON TRANSPORT / four-helix bundle | ||||||
Function / homology | ![]() electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tezcan, F.A. / Medina-Morales, A.M. / Perez, A. / Brodin, J.D. | ||||||
![]() | ![]() Title: In Vitro and Cellular Self-Assembly of a Zn-Binding Protein Cryptand via Templated Disulfide Bonds. Authors: Medina-Morales, A. / Perez, A. / Brodin, J.D. / 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 | ![]() | 215.5 KB | Display | ![]() |
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PDB format | ![]() | 173.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 28.4 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4je9C ![]() 4jebC ![]() 3iq6S 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
#1: Protein | Mass: 11675.152 Da / Num. of mol.: 4 / Fragment: UNP residues 23-128 Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, K77H, E81C, T96C, R98C, Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.56 % |
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Crystal grow | Temperature: 293 K / pH: 8.5 Details: 35% methyl-pentanediol, 0.1M Tris pH 8.5, 0.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 30, 2012 / Details: K-B FOCUSING MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.215→73.422 Å / Num. obs: 129615 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rsym value: 0.046 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.22→1.28 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.568 / % possible all: 83 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IQ6 Resolution: 1.22→31.94 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 1.245 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
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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: 26.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→31.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.25 Å / Total num. of bins used: 20
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