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Yorodumi- PDB-1b3h: OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-CYCLOHEXYLALAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b3h | ||||||
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Title | OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-CYCLOHEXYLALANYL-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: 2 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 | 1b3h.cif.gz | 120.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b3h.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 1b3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/1b3h ftp://data.pdbj.org/pub/pdb/validation_reports/b3/1b3h | HTTPS FTP |
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-Related structure data
Related structure data | 1b0hC 1b1hC 1b2hC 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: 429.597 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Chemical | ChemComp-U1 / #4: 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: 2.45 Å3/Da / Density % sol: 49.81 % | |||||||||||||||||||||||||
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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: 2→20 Å / Num. obs: 38674 / % possible obs: 98 % / Redundancy: 6 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 3.7 |
Reflection | *PLUS % possible obs: 98.3 % / Num. measured all: 231066 |
Reflection shell | *PLUS % possible obs: 91.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.239 / Rfactor Rwork: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |