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Yorodumi- PDB-6zv9: Terbium(III)-bound de novo TIM barrel-ferredoxin fold fusion dime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zv9 | ||||||
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Title | Terbium(III)-bound de novo TIM barrel-ferredoxin fold fusion dimer with 4-glutamate binding site and tryptophan antenna (TFD-EE N6W) | ||||||
Components | TFD-EE | ||||||
Keywords | DE NOVO PROTEIN / Lanthanide-binding protein | ||||||
Function / homology | TERBIUM(III) ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Caldwell, S. / Haydon, I. / Piperidou, N. / Huang, P. / Hilvert, D. / Baker, D. / Zeymer, C. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion. Authors: Caldwell, S.J. / Haydon, I.C. / Piperidou, N. / Huang, P.S. / Bick, M.J. / Sjostrom, H.S. / Hilvert, D. / Baker, D. / Zeymer, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zv9.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zv9.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zv9_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6zv9_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6zv9_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 6zv9_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/6zv9 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/6zv9 | HTTPS FTP |
-Related 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: 18906.947 Da / Num. of mol.: 2 / Mutation: N6W Source method: isolated from a genetically manipulated source Details: The first four amino acids (GAMG) are not part of the de novo designed sequence, but a results of the cloning and purification strategy. They are thus numbered -3, -2, -1, 0. Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-TB / | #3: Chemical | ChemComp-EDO / | #4: 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: 2.29 Å3/Da / Density % sol: 46.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M HEPES pH 7.5, 20 % PEG 4000, and 10 % iso-propanol, containing Gly3 as an additive |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 56427 / % possible obs: 98.4 % / Redundancy: 3.06 % / CC1/2: 0.999 / Rrim(I) all: 0.055 / Net I/σ(I): 13.12 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.97 % / Mean I/σ(I) obs: 1.94 / Num. unique obs: 8189 / CC1/2: 0.845 / Rrim(I) all: 0.697 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Single domain Rosetta models Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 9.792 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.69 Å2 / Biso mean: 47.312 Å2 / Biso min: 22.11 Å2
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Refinement step | Cycle: final / Resolution: 1.85→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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