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Yorodumi- PDB-5t0w: Crystal structure of the ancestral amino acid-binding protein Anc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t0w | ||||||
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Title | Crystal structure of the ancestral amino acid-binding protein AncCDT-1, a precursor of cyclohexadienyl dehydratase | ||||||
Components | AncCDT-1 | ||||||
Keywords | TRANSPORT PROTEIN / solute-binding protein / periplasmic binding protein / transport / amino acid | ||||||
Function / homology | ARGININE Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Clifton, B.E. / Carr, P.D. / Jackson, C.J. | ||||||
Citation | Journal: To Be Published Title: To be published Authors: Clifton, B.E. / Kaczmarski, J.A. / Carr, P.D. / Jackson, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t0w.cif.gz | 358.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t0w.ent.gz | 295.1 KB | Display | PDB format |
PDBx/mmJSON format | 5t0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t0w_validation.pdf.gz | 470.9 KB | Display | wwPDB validaton report |
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Full document | 5t0w_full_validation.pdf.gz | 483.7 KB | Display | |
Data in XML | 5t0w_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 5t0w_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/5t0w ftp://data.pdbj.org/pub/pdb/validation_reports/t0/5t0w | HTTPS FTP |
-Related structure data
Related structure data | 4zv2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 14 - 246 / Label seq-ID: 14 - 246
NCS ensembles :
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Details | Monomer confirmed by size-exclusion chromatography |
-Components
#1: Protein | Mass: 27779.801 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pDOTS7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) #2: Chemical | ChemComp-ARG / #3: 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: 2.46 Å3/Da / Density % sol: 49.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: A crystal grown in a hanging drop of 2 uL protein (18 mg/mL in 20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM arginine) + 2 uL precipitant (0.2 M lithium sulfate, 0.1 M TRIS pH 8.2, 22% (w/v) PEG 3350) ...Details: A crystal grown in a hanging drop of 2 uL protein (18 mg/mL in 20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM arginine) + 2 uL precipitant (0.2 M lithium sulfate, 0.1 M TRIS pH 8.2, 22% (w/v) PEG 3350) was improved by three rounds of serial microseeding; the crystals were crushed and serially diluted in the precipitant, and new hanging drops were prepared by mixing 2 uL protein and 2 uL microseed suspension. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9501 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9501 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→33.66 Å / Num. obs: 33106 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 29.2 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.158 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.59→2.71 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.755 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZV2 Resolution: 2.59→33.19 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.863 / SU B: 31.219 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 0.971 / ESU R Free: 0.359 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 43.419 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→33.19 Å
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Refine LS restraints |
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