+Open data
-Basic information
Entry | Database: PDB / ID: 1r9l | |||||||||
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Title | structure analysis of ProX in complex with glycine 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 / hyperosmotic response / cellular response to osmotic stress / 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 / hyperosmotic response / cellular response to osmotic stress / 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 / SYNCHROTRON / MIR / Resolution: 1.59 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 | 1r9l.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r9l.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 1r9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r9l_validation.pdf.gz | 420.4 KB | Display | wwPDB validaton report |
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Full document | 1r9l_full_validation.pdf.gz | 420.6 KB | Display | |
Data in XML | 1r9l_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1r9l_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/1r9l ftp://data.pdbj.org/pub/pdb/validation_reports/r9/1r9l | 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: 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-BET / |
#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: 1.89 Å3/Da / Density % sol: 33.36 % | ||||||||||||||||||||||||||||||
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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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8439 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 11, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8439 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→15 Å / Num. all: 40866 / Num. obs: 40866 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.57→1.67 Å / % possible all: 95.2 |
Reflection | *PLUS Num. measured all: 142884 / Rmerge(I) obs: 0.026 |
Reflection shell | *PLUS % possible obs: 95.2 % / Rmerge(I) obs: 0.047 / Mean I/σ(I) obs: 18.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.59→12.26 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.59→12.26 Å
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LS refinement shell | Resolution: 1.6→1.65 Å / Rfactor Rfree error: 0
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Refinement | *PLUS Rfactor Rwork: 0.15 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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