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Yorodumi- PDB-1z16: Crystal structure analysis of periplasmic Leu/Ile/Val-binding pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z16 | ||||||
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Title | Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound leucine | ||||||
Components | Leu/Ile/Val-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / periplasmic binding proteins / alpha-beta fold / aliphatic amino acid binding protein | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Trakhanov, S.D. / Vyas, N.K. / Kristensen, D.M. / Ma, J. / Quiocho, F.A. | ||||||
Citation | Journal: Biochemistry / Year: 2005 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: Journal: J.Mol.Biol. / Year: 1989 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: Journal: J.Mol.Biol. / Year: 1989 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z16.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z16.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 1z16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/1z16 ftp://data.pdbj.org/pub/pdb/validation_reports/z1/1z16 | 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: 36812.395 Da / Num. of mol.: 1 / Fragment: matured protein (residues 24-367) / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P02917, UniProt: P0AD96*PLUS |
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#2: Chemical | ChemComp-CD / |
#3: Chemical | ChemComp-LEU / |
#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: 2.79 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 40 % MPD, 20mM Na-acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Mar 17, 1992 / Details: Graphite monochromator |
Radiation | Monochromator: Graphite monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. all: 78881 / Num. obs: 51535 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.72→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5567 / Rsym value: 0.25 / % possible all: 24 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: LIV domains Resolution: 1.72→35.2 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 156923.79 / 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: 62.1794 Å2 / ksol: 0.388302 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.72→35.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.83 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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