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Yorodumi- PDB-5vjt: De Novo Photosynthetic Reaction Center Protein Equipped with Heme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vjt | ||||||
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Title | De Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Zn(II) cations | ||||||
Components | Reaction Center Maquette | ||||||
Keywords | DE NOVO PROTEIN / maquette / protein design / charge separation / artificial photosynthesis | ||||||
Function / homology | PROTOPORPHYRIN IX CONTAINING FE Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å | ||||||
Authors | Ennist, N.M. / Stayrook, S.E. / Dutton, P.L. / Moser, C.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: De novo protein design of photochemical reaction centers. Authors: Ennist, N.M. / Zhao, Z. / Stayrook, S.E. / Discher, B.M. / Dutton, P.L. / Moser, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vjt.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vjt.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 5vjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/5vjt ftp://data.pdbj.org/pub/pdb/validation_reports/vj/5vjt | HTTPS FTP |
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-Related structure data
-Links
-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: 22530.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: de novo designed protein / Source: (gene. exp.) synthetic construct (others) / Gene: designed / Plasmid: pJ414 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.82 % / Description: octahedron |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 2.7 M NaCl, 100 mM Na acetate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2013 / Details: Oxford Danfysik toroidal focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→41.21 Å / Num. obs: 43568 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.779 % / Biso Wilson estimate: 23.325 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.105 / Χ2: 0.953 / Net I/σ(I): 15.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→41.21 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.103 / SU ML: 0.072 / SU R Cruickshank DPI: 0.0699 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.074 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.57 Å2 / Biso mean: 23.274 Å2 / Biso min: 11.18 Å2
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Refinement step | Cycle: final / Resolution: 1.45→41.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.452→1.489 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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