+Open data
-Basic information
Entry | Database: PDB / ID: 2olb | |||||||||
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Title | OLIGOPEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH TRI-LYSINE | |||||||||
Components |
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Keywords | COMPLEX (BINDING PROTEIN/PEPTIDE) / PERIPLASMIC / COMPLEX (BINDING PROTEIN-PEPTIDE) COMPLEX | |||||||||
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 / SYNCHROTRON / Resolution: 1.4 Å | |||||||||
Authors | Tame, J. / Wilkinson, A.J. | |||||||||
Citation | 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. #1: 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. #2: Journal: Science / Year: 1994 Title: The Structural Basis of Sequence-Independent Peptide Binding by Oppa Protein Authors: Tame, J.R.H. / Murshudov, G. / Neil, T. / Dodson, E. / Dodson, G.G. / Higgins, C.F. / Wilkinson, A.J. | |||||||||
History |
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Remark 700 | SHEET THE HELIX AND SHEET RECORDS PRESENTED HERE ARE SIMPLIFIED TO HELP NAVIGATE AROUND THE PROTEIN ...SHEET THE HELIX AND SHEET RECORDS PRESENTED HERE ARE SIMPLIFIED TO HELP NAVIGATE AROUND THE PROTEIN AND TO AVOID OBSCURING TOPOLOGICAL RELATIONSHIPS WITH RELATED PROTEINS. IT IS NOT INTENDED TO REPLACE THE LIST WHICH THE PDB HAS GENERATED USING DSSP WHICH APPEAR ON ACTUAL HELIX AND SHEET RECORDS FURTHER DOWN IN THE ENTRY. BECAUSE OF LINE LENGTH LIMITATIONS THE FORMAT OF THE SHEET INFORMATION PRESENTED IN THIS REMARK HAS BEEN MODIFIED. HELIX 1 1 VAL A 34 LEU A 43 1 HELIX 2 2 HIS A 91 ALA A 101 1 HELIX 3 3 TYR A 112 GLY A 116 1 HELIX 4 4 ILE A 121 ALA A 126 1 HELIX 5 5 LYS A 169 PHE A 175 1 HELIX 6 6 GLU A 229 SER A 238 1 HELIX 7 7 ILE A 250 GLU A 259 1 HELIX 8 8 VAL A 287 ALA A 296 1 HELIX 9 9 ARG A 299 LYS A 305 1 HELIX 10 10 GLN A 337 ALA A 351 1 HELIX 11 11 ASP A 369 LEU A 386 1 HELIX 12 12 TRP A 397 GLN A 406 1 HELIX 13 13 THR A 424 LEU A 427 1 HELIX 14 14 PRO A 444 LYS A 455 1 HELIX 15 15 ASP A 459 ASP A 476 1 SH 1 A 7 VAL A 264 PRO A 268 0 SH 2 A 7 VAL A 486 LEU A 490 -1 N ARG A 489 O ARG A 265 SH 3 A 7 ASP A 242 TYR A 245 -1 N THR A 244 O LEU A 490 SH 4 A 7 THR A 14 ASN A 18 1 N ASN A 18 O MET A 243 SH 5 A 7 GLN A 220 LEU A 224 1 N GLN A 220 O LEU A 15 SH 6 A 7 ARG A 201 ARG A 206 -1 N LEU A 204 O VAL A 221 SH 7 A 7 TYR A 191 VAL A 197 -1 N VAL A 197 O ARG A 201 SH 1 B 4 ALA A 61 LYS A 67 0 SH 2 B 4 VAL A 71 LEU A 76 -1 N HIS A 75 O GLU A 62 SH 3 B 4 THR A 143 THR A 147 -1 N VAL A 146 O TRP A 72 SH 4 B 4 VAL A 136 ASP A 140 -1 N ASP A 140 O THR A 143 SH 1 C 5 ASN A 389 GLN A 395 0 SH 2 C 5 THR A 360 ASN A 366 1 O TYR A 365 N GLN A 395 SH 3 C 5 VAL A 411 CYS A 417 1 O VAL A 411 N LEU A 364 SH 4 C 5 CYS A 271 ILE A 277 -1 N GLU A 276 O ALA A 412 SH 5 C 5 ILE A 479 TYR A 484 -1 N TYR A 483 O TYR A 273 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2olb.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2olb.ent.gz | 103 KB | Display | PDB format |
PDBx/mmJSON format | 2olb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/2olb ftp://data.pdbj.org/pub/pdb/validation_reports/ol/2olb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 283 |
-Components
#1: Protein | Mass: 58878.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / References: UniProt: P06202 | ||||||
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#2: Protein/peptide | Mass: 405.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CO-CRYSTALLIZED WITH URANIUM ACETATE | ||||||
#3: Chemical | ChemComp-IUM / #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | Nonpolymer details | FIVE OF THE EIGHT URANIUM IONS HAVE ASSOCIATED OXYGEN ATOMS IN THE MODEL. THE GEOMETRY OF THESE ...FIVE OF THE EIGHT URANIUM IONS HAVE ASSOCIATED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.99 % Description: THE DATA SET USED WAS COLLECTED FROM MORE THAN ONE CRYSTAL, AS DESCRIBED IN THE JRNL ARTICLE | ||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.36→17.96 Å / Num. obs: 109232 / % possible obs: 88.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.097 | |||||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.097 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 84.2 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Resolution: 1.4→10 Å / σ(F): 0 Details: SIX ACETATE IONS HAVE BEEN MODELED INTO THE ELECTRON DENSITY. ACETATE 1 IS FOUND AT THE SAME POSITION AS THE CARBOXYL GROUP OF A BOUND TETRAPEPTIDE LIGAND. ACETATE 2 IS FOUND AT THE POSITION ...Details: SIX ACETATE IONS HAVE BEEN MODELED INTO THE ELECTRON DENSITY. ACETATE 1 IS FOUND AT THE SAME POSITION AS THE CARBOXYL GROUP OF A BOUND TETRAPEPTIDE LIGAND. ACETATE 2 IS FOUND AT THE POSITION WHERE THE CARBOXYL GROUP OF A BOUND PENTAPEPTIDE LIGAND IS BELIEVED TO LIE. THE REMAINING ACETATES ARE FOUND AT THE SURFACE CLOSE TO URANYL IONS AND HAVE RELATIVELY POOR DENSITY. SOLVENT STRUCTURE AROUND THE URANYL IONS IS TENTATIVE.
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Displacement parameters | Biso mean: 14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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