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Yorodumi- PDB-1b0h: OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-NAPTHYLALANYL-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b0h | ||||||
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Title | OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-NAPTHYLALANYL-LYSINE | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / PERIPLASMIC PEPTIDE BINDING PROTEIN | ||||||
Function / homology | Function and homology information peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / protein transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Davies, T.G. / Tame, J.R.H. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes. Authors: Davies, T.G. / Hubbard, R.E. / Tame, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b0h.cif.gz | 124.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b0h.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 1b0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/1b0h ftp://data.pdbj.org/pub/pdb/validation_reports/b0/1b0h | HTTPS FTP |
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-Related structure data
Related structure data | 1b1hC 1b2hC 1b3hC 1b4hC 1b5hC 1b6hC 1b7hC C: citing same article (ref.) |
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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: 58878.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: OPPA_SALTY, UniProt: P06202*PLUS | ||
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#2: Protein/peptide | Mass: 473.608 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | ChemComp-U1 / #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: 2.47 Å3/Da / Density % sol: 50.11 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. obs: 47086 / % possible obs: 98 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 3.8 / % possible all: 98.7 |
Reflection | *PLUS % possible obs: 98.9 % / Num. measured all: 212059 |
Reflection shell | *PLUS % possible obs: 98.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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