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- PDB-1b4h: OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-DIAMINOBUTYRIC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1b4h | ||||||
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Title | OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-DIAMINOBUTYRIC ACID-LYSINE | ||||||
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![]() | PEPTIDE BINDING PROTEIN / PERIPLASMIC PEPTIDE BINDING PROTEIN | ||||||
Function / homology | ![]() peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / protein transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Davies, T.G. / Tame, J.R.H. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.1 KB | Display | ![]() |
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PDB format | ![]() | 94.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376.1 KB | Display | ![]() |
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Full document | ![]() | 382 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b0hC ![]() 1b1hC ![]() 1b2hC ![]() 1b3hC ![]() 1b5hC ![]() 1b6hC ![]() 1b7hC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 376.494 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % | |||||||||||||||||||||||||
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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: ![]() |
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: 47784 / % possible obs: 99.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.3 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. obs: 47784 / % possible obs: 98.7 % / Num. measured all: 221800 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 19.5 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: 0.23 / Rfactor Rwork: 0.19 / Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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