+Open data
-Basic information
Entry | Database: PDB / ID: 1usk | ||||||
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Title | L-leucine-binding protein with leucine bound | ||||||
Components | LEUCINE-SPECIFIC BINDING PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / LEUCINE-BINDING PROTEIN / PROTEIN STRUCTURE / ABC TRANSPORT SYSTEMS | ||||||
Function / homology | Function and homology information branched-chain amino acid transport / L-leucine binding / phenylalanine transport / L-leucine transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Magnusson, U. / Salopek-Sondi, B. / Luck, L.A. / Mowbray, S.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: X-Ray Structures of the Leucine-Binding Protein Illustrate Conformational Changes and the Basis of Ligand Specificity Authors: Magnusson, U. / Salopek-Sondi, B. / Luck, L.A. / Mowbray, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1usk.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1usk.ent.gz | 210.7 KB | Display | PDB format |
PDBx/mmJSON format | 1usk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/1usk ftp://data.pdbj.org/pub/pdb/validation_reports/us/1usk | HTTPS FTP |
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-Related structure data
Related structure data | 1usgC 1usiSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 37079.699 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKSTY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P04816 #2: Chemical | ChemComp-LEU / #3: Water | ChemComp-HOH / | Compound details | A COMPONENT OF THE LEUCINE-SPECIFIC TRANSPORT SYSTEM, WHICH IS ONE OF TWO PERIPLASMIC BINDING ...A COMPONENT OF THE LEUCINE-SPECIFIC TRANSPORT SYSTEM, WHICH IS ONE OF TWO PERIPLASMI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: PEG 4000, SODIUM CITRATE, PH 5.6, 2-PROPANOL | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
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: MAX II / Beamline: I711 / Wavelength: 0.98 |
Detector | Date: Mar 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→38 Å / Num. obs: 72985 / % possible obs: 79.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.4 / % possible all: 22.7 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.164 |
Reflection shell | *PLUS % possible obs: 22.7 % / Redundancy: 1.1 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1USI Resolution: 2→72.55 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.129 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.217 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2→72.55 Å
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Refine LS restraints |
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