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Yorodumi- PDB-1b2h: Oligo-Peptide Binding Protein Complexed with Lysyl-Ornithyl-Lysine -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b2h | ||||||
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Title | Oligo-Peptide Binding Protein Complexed with Lysyl-Ornithyl-Lysine | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN | ||||||
Function / homology | Function and homology information peptide transmembrane transporter activity / peptide transport / 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. #1: Journal: Structure / Year: 1995 Title: The Crystal Structures of the Oligopeptide-Binding Protein Oppa Complexed with Tripeptide and Tetrapeptide Ligands Authors: Tame, J.R. / Dodson, E.J. / Murshudov, G. / Higgins, C.F. / Wilkinson, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b2h.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b2h.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 1b2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b2h_validation.pdf.gz | 384.8 KB | Display | wwPDB validaton report |
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Full document | 1b2h_full_validation.pdf.gz | 392.1 KB | Display | |
Data in XML | 1b2h_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1b2h_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/1b2h ftp://data.pdbj.org/pub/pdb/validation_reports/b2/1b2h | HTTPS FTP |
-Related structure data
Related structure data | 1b0hC 1b1hC 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: P06202 | ||||
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#2: Protein/peptide | Mass: 390.521 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Chemical | ChemComp-ACT / | ||||
#4: Chemical | ChemComp-U1 / #5: Water | ChemComp-HOH / | Nonpolymer details | THE SOLVENT STRUCTURE AROUND THE URANIUM IONS IS TENTATIVE | |
-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: 50.24 % | |||||||||||||||||||||||||
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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→20 Å / Num. obs: 46360 / % possible obs: 98.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 6 |
Reflection shell | *PLUS % possible obs: 90.4 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 4.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.218 / Rfactor Rwork: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.029 |