+Open data
-Basic information
Entry | Database: PDB / ID: 1b5j | ||||||
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Title | OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KQK | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / COMPLEX (PEPTIDE TRANSPORT-PEPTIDE) / PEPTIDE TRANSPORT | ||||||
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 / OTHER / Resolution: 1.8 Å | ||||||
Authors | Tame, J.R.H. / Wilkinson, A.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 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. #1: Journal: Nat.Struct.Biol. / Year: 1996 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: Journal: Structure / Year: 1995 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: Journal: Science / Year: 1994 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b5j.cif.gz | 122.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b5j.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 1b5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b5j_validation.pdf.gz | 369.8 KB | Display | wwPDB validaton report |
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Full document | 1b5j_full_validation.pdf.gz | 373.9 KB | Display | |
Data in XML | 1b5j_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 1b5j_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/1b5j ftp://data.pdbj.org/pub/pdb/validation_reports/b5/1b5j | HTTPS FTP |
-Related structure data
Related structure data | 1b05C 1b32C 1b3fC 1b3gC 1b3lC 1b40C 1b46C 1b4zC 1b51C 1b52C 1b58C 1b5iC 1b9jC 1qkaC 1qkbC 1olb S: Starting model for refinement 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) / Gene: OPPA / Production host: Escherichia coli (E. coli) / References: UniProt: P06202 | ||||
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#2: Protein/peptide | Mass: 404.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | ChemComp-U1 / #4: Water | ChemComp-HOH / | Nonpolymer details | SEVERAL WATER MOLECULES IN THE MODEL HAVE LOW TEMPERATURE FACTORS BUT FORM NO HYDROGEN BONDS. THESE ...SEVERAL WATER MOLECULES IN THE MODEL HAVE LOW TEMPERATUR | |
-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: 45 % / Description: FLASH COOLED TO 120K | |||||||||||||||||||||||||
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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 | Wavelength: 1.54 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 54587 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.3 / % possible all: 66.7 |
Reflection | *PLUS Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1OLB 1olb Resolution: 1.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 25.7 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 Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |