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Yorodumi- PDB-5l32: Crystal structure of the Zn-RIDC1 complex bearing six interfacial... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l32 | |||||||||
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Title | Crystal structure of the Zn-RIDC1 complex bearing six interfacial disulfide bonds | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | METAL BINDING PROTEIN / protein engineering / metalloprotein / cytochrome / disulfide bonding | |||||||||
Function / homology | Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transfer activity / periplasmic space / iron ion binding / heme binding / HEME C / Soluble cytochrome b562 Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Churchfield, L.A. / Tezcan, F.A. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l32.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l32.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 5l32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/5l32 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/5l32 | HTTPS FTP |
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-Related structure data
Related structure data | 5l31C 3hnjS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Escherichia coli (E. coli) / Gene: cybC / Plasmid: Plasmid / Details (production host): pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ABE7 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.98 Å |
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: 0.98 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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