+Open data
-Basic information
Entry | Database: PDB / ID: 1b9j | ||||||
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Title | OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KLK | ||||||
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) synthetic construct (others) | ||||||
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. / 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. / 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 A resolution using multiple-wavelength anomalous dispersion methods. Authors: Glover, I.D. / Denny, R.C. / Nguti, N.D. / McSweeney, S.M. / Kinder, S.H. / Thompson, A.W. / Dodson, E.J. / Wilkinson, A.J. / Tame, J.R. #4: Journal: Science / Year: 1994 Title: The structural basis of sequence-independent peptide binding by OppA protein. Authors: Tame, J.R. / 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 | 1b9j.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b9j.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 1b9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b9j_validation.pdf.gz | 442.3 KB | Display | wwPDB validaton report |
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Full document | 1b9j_full_validation.pdf.gz | 448 KB | Display | |
Data in XML | 1b9j_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 1b9j_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/1b9j ftp://data.pdbj.org/pub/pdb/validation_reports/b9/1b9j | HTTPS FTP |
-Related structure data
Related structure data | 1b05C 1b32C 1b3fC 1b3gC 1b3lC 1b40C 1b46C 1b4zC 1b51C 1b52C 1b58C 1b5iC 1b5jC 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: 389.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | ChemComp-IUM / #4: Water | ChemComp-HOH / | Has protein modification | Y | |
-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: 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 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: 55029 / % possible obs: 90.94 % / Observed criterion σ(I): 0 / Redundancy: 17 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.048 / Mean I/σ(I) obs: 5.3 / % possible all: 55.6 |
Reflection shell | *PLUS % possible obs: 55.6 % |
-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: 23.1 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: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |