+Open data
-Basic information
Entry | Database: PDB / ID: 6vp2 | ||||||
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Title | Artificial Metalloproteins with Dinuclear Iron Centers | ||||||
Components | Streptavidin | ||||||
Keywords | METAL BINDING PROTEIN / Biotin binding Artificial Metalloprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | 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 | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vp2.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vp2.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 6vp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/6vp2 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/6vp2 | HTTPS FTP |
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-Related structure data
Related structure data | 6vo9C 6vobC 6vozC 6vp1C 6vp3C 7kbyC 7kbzC 7knlC 2qcbS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16561.932 Da / Num. of mol.: 4 / Mutation: K121A, L124Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 #2: Chemical | ChemComp-KM3 / { #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 2.0 M ammonium sulfate, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→55.06 Å / Num. obs: 55911 / % possible obs: 99.6 % / Redundancy: 6.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.056 / Rrim(I) all: 0.146 / Net I/σ(I): 10.2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QCB Resolution: 1.8→55.06 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.182 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.104 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: 71.42 Å2 / Biso mean: 16.699 Å2 / Biso min: 8.07 Å2
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Refinement step | Cycle: final / Resolution: 1.8→55.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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