+Open data
-Basic information
Entry | Database: PDB / ID: 4zv1 | ||||||
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Title | An ancestral arginine-binding protein bound to arginine | ||||||
Components | AncQR | ||||||
Keywords | SOLUTE-BINDING PROTEIN / periplasmic binding protein / solute 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: 1.52 Å | ||||||
Authors | Clifton, B.E. / Carr, P.D. / Jackson, C.J. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2016 Title: Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins. Authors: Clifton, B.E. / 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 | 4zv1.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zv1.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zv1_validation.pdf.gz | 438.9 KB | Display | wwPDB validaton report |
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Full document | 4zv1_full_validation.pdf.gz | 440.9 KB | Display | |
Data in XML | 4zv1_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 4zv1_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/4zv1 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/4zv1 | HTTPS FTP |
-Related structure data
Related structure data | 4zv2C 1wdnS 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: 25725.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pETMCSIII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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#2: Chemical | ChemComp-ARG / |
#3: 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: 2.53 Å3/Da / Density % sol: 51.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M Li2SO4, 0.1 M HEPES pH 7.5, 27.5% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→28.56 Å / Num. obs: 40887 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.52→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.4 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WDN Resolution: 1.52→28.56 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.261 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.732 Å2
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Refinement step | Cycle: 1 / Resolution: 1.52→28.56 Å
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Refine LS restraints |
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