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- PDB-1z15: Crystal structure analysis of periplasmic Leu/Ile/Val-binding pro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1z15 | ||||||
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Title | Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein in superopen form | ||||||
![]() | Leu/Ile/Val-binding protein | ||||||
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Function / homology | ![]() branched-chain amino acid transport / isoleucine transport / valine transport / L-leucine transport / amino acid transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Trakhanov, S.D. / Vyas, N.K. / Kristensen, D.M. / Ma, J. / Quiocho, F.A. | ||||||
![]() | ![]() Title: Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity. Authors: Trakhanov, S.D. / Vyas, N.K. / Luecke, H. / Kristensen, D.M. / Ma, J. / Quiocho, F.A. #1: ![]() Title: Periplasmic binding protein structure and function. Refined X-ray structures of the leucine/isoleucine/valine-binding protein and its complex with leucine. Authors: Sack, J.S. / Saper, M.A. / Quiocho, F.A. #2: ![]() Title: Structure of the L-leucine-binding protein refined at 2.4 A resolution and comparison with the Leu/Ile/Val-binding protein structure Authors: Sack, J.S. / Trakhanov, S.D. / Tsigannik, I.H. / Quiocho, F.A. | ||||||
History |
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Remark 999 | SEQUENCE This sequence occurs with n-terminal leader sequence, which is modified post translation ... SEQUENCE This sequence occurs with n-terminal leader sequence, which is modified post translation to produce a mature protein |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.4 KB | Display | ![]() |
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PDB format | ![]() | 60.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1z16C ![]() 1z17C ![]() 1z18C ![]() 2livS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36812.395 Da / Num. of mol.: 1 / Fragment: matured protein (residues 24-367) / Source method: isolated from a natural source / Details: Periplasmic / Source: (natural) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55 % |
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Crystal grow![]() | Temperature: 293 K / Method: microdialysis / pH: 7.3 Details: 12.5% PEG 6000, potassium chloride, sodium choloride, sodium azide, potassium acetate, sodium citrate, pH 7.3, MICRODIALYSIS, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jan 10, 1990 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→50 Å / Num. all: 44773 / Num. obs: 44773 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 4 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4655 / Rsym value: 0.277 / % possible all: 89 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2LIV Resolution: 1.7→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2081291.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 111.766 Å2 / ksol: 0.41215 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.8 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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