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Open data
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Basic information
Entry | Database: PDB / ID: 1qka | ||||||
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Title | OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KRK | ||||||
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![]() | PROTEIN TRANSPORT / COMPLEX (PEPTIDE TRANSPORT-PEPTIDE) / PEPTIDE TRANSPORT | ||||||
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 | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Tame, J.R.H. / Wilkinson, A.J. | ||||||
![]() | ![]() Title: Crystallographic and Calorimetric Analysis of Peptide Binding to Oppa Protein Authors: Sleigh, S.H. / Seavers, P.R. / Wilkinson, A.J. / Ladbury, J.E. / Tame, J.R.H. #1: ![]() Title: The Role of Water in Sequence-Independent Ligand Binding by an Oligopeptide Transporter Protein Authors: Tame, J.R.H. / Sleigh, S.H. / Wilkinson, A.J. / Ladbury, J.E. #2: ![]() Title: The Crystal Structures of the Oligopeptide-Binding Protein Oppa Complexed with Tripeptide and Tetrapeptide Ligands Authors: Tame, J.R.H. / Dodson, E.J. / Murshudov, G. / Higgins, C.F. / Wilkinson, A.J. #3: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Structure Determination of Oppa at 2.3 Angstroms Resolution Using Multiple Wavelength Anomalous Methods Authors: Glover, I.D. / Denny, R. / Nguti, N.D. / Mcsweeney, S. / Thompson, A. / Dodson, E. / Wilkinson, A.J. / Tame, J.R.H. #4: ![]() Title: The Structural Basis of Sequence-Independent Peptide Binding by Oppa Protein Authors: Tame, J.R.H. / Murshudov, G.N. / Dodson, E.J. / Neil, T.K. / Dodson, G.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 | ![]() | 130.2 KB | Display | ![]() |
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PDB format | ![]() | 98.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 378.8 KB | Display | ![]() |
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Full document | ![]() | 382.5 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b05C ![]() 1b32C ![]() 1b3fC ![]() 1b3gC ![]() 1b3lC ![]() 1b40C ![]() 1b46C ![]() 1b4zC ![]() 1b51C ![]() 1b52C ![]() 1b58C ![]() 1b5iC ![]() 1b5jC ![]() 1b9jC ![]() 1qkbC ![]() 1olb C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 433.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | ChemComp-IUM / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 45 % / Description: FLASH COOLED TO 120K | |||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
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: ![]() |
Detector | Type: R-AXIS IIC / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 52404 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.2 / % possible all: 72.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OLB ![]() 1olb Resolution: 1.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: SEVERAL WATER MOLECULES IN THE MODEL HAVE LOW TEMPERATURE FACTORS BUT FORM NO HYDROGEN BONDS. THESE MAY IN FACT BE URANYL IONS AT LOW OCCUPANCY.
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Displacement parameters | Biso mean: 20.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |