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Yorodumi- PDB-5fio: DARPins as a new tool for experimental phasing in protein crystal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fio | |||||||||
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Title | DARPins as a new tool for experimental phasing in protein crystallography | |||||||||
Components |
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Keywords | METAL BINDING PROTEIN / DARPIN / ENGINEERED PROTEIN / EXPERIMENTAL PHASING | |||||||||
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 | SYNTHETIC CONSTRUCT (others) ESCHERICHIA COLI (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | |||||||||
Authors | Batyuk, A. / Honegger, A. / Andres, F. / Briand, C. / Gruetter, M. / Plueckthun, A. | |||||||||
Citation | Journal: To be Published Title: Darpins as a New Tool for Experimental Phasing in Protein Crystallography Authors: Batyuk, A. / Honegger, A. / Andres, F. / Briand, C. / Gruetter, M. / Plueckthun, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fio.cif.gz | 298.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fio.ent.gz | 256.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/5fio ftp://data.pdbj.org/pub/pdb/validation_reports/fi/5fio | 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: 18583.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DESIGNED ANKYRIN REPEAT PROTEIN WITH THREE INTERNAL REPEAT AND C-TERMINAL CAPPING REPEAT TYPE MUT5 AND ENGINEERED BURIED MERCURY BINDING SITE CYS30-CYS65 WITH BOUND HG-ION Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE30SS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE |
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#2: Protein | Mass: 43187.715 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 29-392 Source method: isolated from a genetically manipulated source Details: INVOLVED IN THE HIGH-AFFINITY MALTOSE MEMBRANE TRANSPORT SYSTEM MALEFGK. INITIAL RECEPTOR FOR THE ACTIVE TRANSPORT OF AND CHEMOTAXIS TOWARD MALTOOLIGOSACCHARIDES. Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PQE30SS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE / References: UniProt: P0AEY0, UniProt: P0AEX9*PLUS |
#3: Chemical | ChemComp-HG / |
#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: 2.14 Å3/Da / Density % sol: 42.64 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 30.55% W/V PEG 6000, 0.1M TRIS-CL, PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00745 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2011 / Details: RH COATED MERIDIONALLY FOCUSSING MIRROR |
Radiation | Monochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00745 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.18 Å / Num. obs: 28809 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.92 |
Reflection shell | Highest resolution: 2.1 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.21 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.1→45.178 Å / SU ML: 0.28 / σ(F): 0.86 / Phase error: 27.46 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→45.178 Å
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Refine LS restraints |
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LS refinement shell |
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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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