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- PDB-1z18: 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: 1z18 | ||||||
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Title | Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound valine | ||||||
![]() | Leu/Ile/Val-binding protein | ||||||
![]() | TRANSPORT PROTEIN / periplasmic binding proteins / alpha-beta fold / aliphatic amino acid binding protein | ||||||
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 / periplasmic space / membrane 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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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.5 KB | Display | ![]() |
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PDB format | ![]() | 60.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1z15C ![]() 1z16SC ![]() 1z17C C: citing same article ( S: Starting model for refinement |
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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 / Source: (natural) ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-VAL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% (v/v) PEG-400, 0.1 M succinic acid, 50 mM CdSo4 and 50 mM Na-cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 5, 1998 / Details: Graphite monochromator |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 45340 / Num. obs: 18896 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 0.5 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.2 / Num. unique all: 18896 / Rsym value: 0.242 / % possible all: 85 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: liv-leu complex without bound leu and solvent, pdb entry 1Z16 Resolution: 2.1→29.21 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 91698.33 / 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: 54.2742 Å2 / ksol: 0.381888 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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