+Open data
-Basic information
Entry | Database: PDB / ID: 4zv2 | ||||||
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Title | An ancestral arginine-binding protein bound to glutamine | ||||||
Components | AncQR | ||||||
Keywords | SOLUTE-BINDING PROTEIN / periplasmic binding protein / solute binding protein / transport / amino acid | ||||||
Function / homology | GLUTAMINE Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Clifton, B.E. / 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 | 4zv2.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zv2.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/4zv2 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/4zv2 | HTTPS FTP |
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-Related structure data
Related structure data | 4zv1SC 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
#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-GLN / |
#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: 2.26 Å3/Da / Density % sol: 45.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M MgCl2, 0.1 M HEPES pH 7.5, 24% (w/v) PEG 3350, microseeds from crushed crystals produced using same precipitant |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9655 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9655 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→36.2 Å / Num. obs: 43838 / % possible obs: 99.7 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.871 / Mean I/σ(I) obs: 1.5 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZV1 Resolution: 1.43→34.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.072 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / 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: 15.311 Å2
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Refinement step | Cycle: 1 / Resolution: 1.43→34.21 Å
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Refine LS restraints |
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