+Open data
-Basic information
Entry | Database: PDB / ID: 5wvm | ||||||||||||
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Title | Crystal structure of baeS cocrystallized with 2 mM indole | ||||||||||||
Components | Maltose-binding periplasmic protein,Two-component system sensor kinase | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / BaeS / sensor domain / Indole / two component system | ||||||||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) Serratia marcescens subsp. marcescens Db11 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||||||||
Authors | Wang, W. / Zhang, Y. / Rang, T. / Xu, D. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Proteins / Year: 2017 Title: Crystal structure of the sensor domain of BaeS from Serratia marcescens FS14 Authors: Zhang, Y. / Qiu, S. / Jia, S. / Xu, D. / Ran, T. / Wang, W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wvm.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wvm.ent.gz | 83.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/5wvm ftp://data.pdbj.org/pub/pdb/validation_reports/wv/5wvm | HTTPS FTP |
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-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: 57250.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Serratia marcescens subsp. marcescens Db11 (bacteria) Strain: K12 / Gene: malE, b4034, JW3994, baeS, SMDB11_2949 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: A0A0N1UYP9 | ||
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#2: Chemical | ChemComp-SO4 / #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: 4.68 Å3/Da / Density % sol: 73.71 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Citric Acid: NaOH , 2.0M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: AREA DETECTOR / Date: Dec 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→46.329 Å / Num. obs: 24756 / % possible obs: 100 % / Redundancy: 13.2 % / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.329 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.97 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→46.329 Å
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Refine LS restraints |
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LS refinement shell |
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