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Yorodumi- PDB-4f1v: Subatomic resolution structure of a high affinity periplasmic pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f1v | |||||||||
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Title | Subatomic resolution structure of a high affinity periplasmic phosphate-binding protein (PfluDING) bound with phosphate at pH 8.5 | |||||||||
Components | Putative alkaline phosphatase | |||||||||
Keywords | PHOSPHATE-BINDING PROTEIN / venus flytrap / phosphate binding protein / pstS / DING | |||||||||
Function / homology | Function and homology information phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex / extracellular region Similarity search - Function | |||||||||
Biological species | Pseudomonas fluorescens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.88 Å | |||||||||
Authors | Liebschner, D. / Elias, M. / Tawfik, D.S. / Moniot, S. / Fournier, B. / Scott, K. / Jelsch, C. / Guillot, B. / Lecomte, C. / Chabriere, E. | |||||||||
Citation | Journal: Nature / Year: 2012 Title: The molecular basis of phosphate discrimination in arsenate-rich environments. Authors: Elias, M. / Wellner, A. / Goldin-Azulay, K. / Chabriere, E. / Vorholt, J.A. / Erb, T.J. / Tawfik, D.S. #1: Journal: J.Am.Chem.Soc. / Year: 2009 Title: Elucidation of the phosphate binding mode of DING proteins revealed by subangstrom X-ray crystallography. Authors: Liebschner, D. / Elias, M. / Moniot, S. / Fournier, B. / Scott, K. / Jelsch, C. / Guillot, B. / Lecomte, C. / Chabriere, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f1v.cif.gz | 374 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f1v.ent.gz | 307.9 KB | Display | PDB format |
PDBx/mmJSON format | 4f1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/4f1v ftp://data.pdbj.org/pub/pdb/validation_reports/f1/4f1v | HTTPS FTP |
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-Related structure data
Related structure data | 4f18C 4f19C 4f1uC 3g63 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: 39119.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: SBW25 / Gene: PFLU_2427 / Production host: Escherichia coli (E. coli) / References: UniProt: C3K8K1 |
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#2: Chemical | ChemComp-PI / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.17 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.75 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.75 Å / Relative weight: 1 |
Reflection | Resolution: 0.88→62.5 Å / Num. obs: 254891 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3G63 3g63 Resolution: 0.88→62.5 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.534 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 8.308 Å2
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Refinement step | Cycle: LAST / Resolution: 0.88→62.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.88→0.903 Å / Total num. of bins used: 20
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