+Open data
-Basic information
Entry | Database: PDB / ID: 1r9q | ||||||
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Title | structure analysis of ProX in complex with proline betaine | ||||||
Components | Glycine betaine-binding periplasmic protein | ||||||
Keywords | PROTEIN BINDING / periplasmic binding protein / cation-pi interactions / tryptophan box | ||||||
Function / homology | Function and homology information ProVWX complex / glycine import across plasma membrane / glycine betaine transport / quaternary ammonium group binding / amino acid import across plasma membrane / cellular response to osmotic stress / hyperosmotic response / amino acid transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex ...ProVWX complex / glycine import across plasma membrane / glycine betaine transport / quaternary ammonium group binding / amino acid import across plasma membrane / cellular response to osmotic stress / hyperosmotic response / amino acid transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / periplasmic space / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Schiefner, A. / Breed, J. / Bosser, L. / Kneip, S. / Gade, J. / Holtmann, G. / Diederichs, K. / Welte, W. / Bremer, E. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2004 Title: Cation-pi Interactions as Determinants for Binding of the Compatible Solutes Glycine Betaine and Proline Betaine by the Periplasmic Ligand-binding Protein ProX from Escherichia coli Authors: Schiefner, A. / Breed, J. / Bosser, L. / Kneip, S. / Gade, J. / Holtmann, G. / Diederichs, K. / Welte, W. / Bremer, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r9q.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r9q.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 1r9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r9q_validation.pdf.gz | 442.5 KB | Display | wwPDB validaton report |
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Full document | 1r9q_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 1r9q_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1r9q_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/1r9q ftp://data.pdbj.org/pub/pdb/validation_reports/r9/1r9q | HTTPS FTP |
-Related structure data
Related structure data | 1r9lSC 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: 33760.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ProX / Plasmid: pSK7 / Production host: Escherichia coli (E. coli) / Strain (production host): PD141 / References: UniProt: P14177, UniProt: P0AFM2*PLUS |
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#2: Chemical | ChemComp-UNX / |
#3: Chemical | ChemComp-PBE / |
#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: 2.21 Å3/Da / Density % sol: 43.96 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: PEG 4000, PIPES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8.3 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→15 Å / Num. all: 19587 / Num. obs: 19587 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.05→2.25 Å / % possible all: 99.4 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 75377 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 99.4 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 5.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R9L Resolution: 2.05→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.05→10 Å
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LS refinement shell | Resolution: 2.08→2.13 Å / Rfactor Rfree error: 0
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Refinement | *PLUS Lowest resolution: 15 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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