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Yorodumi- PDB-1z17: Crystal structure analysis of periplasmic Leu/Ile/Val-binding pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z17 | ||||||
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Title | Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound ligand isoleucine | ||||||
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: 1.96 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 | 1z17.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z17.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 1z17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/1z17 ftp://data.pdbj.org/pub/pdb/validation_reports/z1/1z17 | HTTPS FTP |
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-Related structure data
Related structure data | 1z15C 1z16SC 1z18C 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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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-ILE / |
#3: Chemical | ChemComp-MRD / ( |
#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: 3.53 Å3/Da / Density % sol: 65.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 30 %MPD, 10mM CuSo4, 0.5 mM Lisoleucine and 50 mM Na-ccodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 14, 1997 / 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: 1.96→50 Å / Num. all: 55719 / Num. obs: 38888 / % possible obs: 83 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 6.8 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.96→2.1 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5412 / Rsym value: 0.184 / % possible all: 40 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: LIVBP-leu complex (closed form) without leucine and solvent, pdb entry 1Z16 Resolution: 1.96→21.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 160361.57 / 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: 51.6541 Å2 / ksol: 0.321657 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.96→21.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.06 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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