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Yorodumi- PDB-3p7i: Crystal structure of Escherichia coli PhnD in complex with 2-amin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p7i | ||||||
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Title | Crystal structure of Escherichia coli PhnD in complex with 2-aminoethyl phosphonate | ||||||
Components | PhnD, subunit of alkylphosphonate ABC transporter | ||||||
Keywords | TRANSPORT PROTEIN / Phosphonate binding protein | ||||||
Function / homology | Function and homology information organic phosphonate transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport Similarity search - Function | ||||||
Biological species | Escherichia coli UTI89 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Alicea, I. / Schreiter, E.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Structure of the Escherichia coli Phosphonate Binding Protein PhnD and Rationally Optimized Phosphonate Biosensors. Authors: Alicea, I. / Marvin, J.S. / Miklos, A.E. / Ellington, A.D. / Looger, L.L. / Schreiter, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p7i.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p7i.ent.gz | 113.3 KB | Display | PDB format |
PDBx/mmJSON format | 3p7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p7i_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 3p7i_full_validation.pdf.gz | 457.4 KB | Display | |
Data in XML | 3p7i_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 3p7i_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/3p7i ftp://data.pdbj.org/pub/pdb/validation_reports/p7/3p7i | 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: 35808.449 Da / Num. of mol.: 1 / Fragment: UNP residues 27-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli UTI89 (bacteria) / Strain: UTI89 / UPEC / Gene: phnD, UTI89_C4699 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1R3F7 | ||
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#2: Chemical | ChemComp-P7I / ( | ||
#3: Chemical | #4: 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: 2.39 Å3/Da / Density % sol: 48.63 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2M ammonium sulfate, sodium acetate trihydrate, pH 4.6, 25% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 16, 2009 |
Radiation | Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→45.6 Å / Num. all: 35864 / Num. obs: 35721 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→45.6 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.12 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.239 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→45.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.757 Å / 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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