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Yorodumi- PDB-1vwi: STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 1.5, I222 COMPLEX -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vwi | ||||||
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Title | STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 1.5, I222 COMPLEX | ||||||
Components |
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Keywords | COMPLEX (BIOTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) / LINEAR THIOETHER-CONTAINING PEPTIDE ENGINEERED / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.5 Å | ||||||
Authors | Katz, B.A. / Cass, R.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1997 Title: In crystals of complexes of streptavidin with peptide ligands containing the HPQ sequence the pKa of the peptide histidine is less than 3.0. Authors: Katz, B.A. / Cass, R.T. #1: Journal: J.Am.Chem.Soc. / Year: 1996 Title: Structure-Based Design Tools: Structural and Thermodynamic Comparison with Biotin of a Small Molecule that Binds Streptavidin with Micromolar Affinity Authors: Katz, B.A. / Liu, B. / Cass, R.T. #2: Journal: J.Am.Chem.Soc. / Year: 1996 Title: Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design Authors: Katz, B.A. #3: Journal: J.Biol.Chem. / Year: 1995 Title: Topochemical Catalysis Achieved by Structure-Based Ligand Design Authors: Katz, B.A. / Cass, R.T. / Liu, B. / Arze, R. / Collins, N. #4: Journal: Chem.Biol. / Year: 1995 Title: Topochemistry for Preparing Ligands that Dimerize Receptors Authors: Katz, B.A. / Stroud, R.M. / Collins, N. / Liu, B. / Arze, R. #5: Journal: Biochemistry / Year: 1995 Title: Binding to Protein Targets of Peptidic Leads Discovered by Phage Display: Crystal Structures of Streptavidin-Bound Linear and Cyclic Peptide Ligands Containing the Hpq Sequence Authors: Katz, B.A. #6: Journal: J.Am.Chem.Soc. / Year: 1995 Title: Structure-Based Design of High Affinity Streptavidin Binding Cyclic Peptide Ligands Containing Thioether Cross-Links Authors: Katz, B.A. / Johnson, C.R. / Cass, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vwi.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vwi.ent.gz | 96.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vwi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/1vwi ftp://data.pdbj.org/pub/pdb/validation_reports/vw/1vwi | HTTPS FTP |
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-Related structure data
Related structure data | 1vwaC 1vwbC 1vwcC 1vwdC 1vweC 1vwfC 1vwgC 1vwhC 1vwjC 1vwkC 1vwlC 1vwmC 1vwnC 1vwoC 1vwpC 1vwqC 1vwrC 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99997, -0.005, 0.005996), Vector: |
-Components
#1: Protein | Mass: 12965.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629 #2: Protein/peptide | Mass: 863.017 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | DISULFIDE BOND OF PHAGE-DISCOVERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 18.7 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 1.5 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M SODIUM FORMATE ADJUSTED TO PH 1.5. | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4 / Method: vapor diffusion, hanging drop / Details: Pahler, A., (1987) J. Biol. Chem., 262, 13933. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 41504 / Redundancy: 2.2 % / Rmerge(I) obs: 0.056 |
Reflection | *PLUS Highest resolution: 1.32 Å / Num. measured all: 89532 |
-Processing
Software |
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Refinement | Resolution: 1.5→7.5 Å / σ(F): 1.8 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 22, B 46, B 47, B 48, B 49, B 50, (TERMINUS OF ARG B 53), (TERMINUS OF ARG B 59), B 62, B 63, B 64, B ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 22, B 46, B 47, B 48, B 49, B 50, (TERMINUS OF ARG B 53), (TERMINUS OF ARG B 59), B 62, B 63, B 64, B 65, B 66, B 67, B 68, (TERMINUS OF ARG B 84), (SIDE CHAIN OF GLU B 101), TERMINUS OF ARG B 103, (CB, HB1, HB2 OF GLU B 116), (CG, HG1, HG2, CD, OE1, OE2 OF GLU B 116), B 135, D 13, D 14, D 15, D 46, D 47, D 48, D 49, D 50, (TERMINUS OF ARG D 53), (TERMINUS OF ARG D 59), D 62, D 63, D 64, D 65, D 66, D 67, D 68, (TERMINUS OF ARG D 84), (TERMINUS OF ARG D 103), (M 9 AND M 10), (P 9 AND P 10). B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A TWO-FOLD RELATED B 22. PROPER REFINEMENT WITH X-PLOR IS NOT POSSIBLE BECAUSE OF THE OVERLAP OF ONE CONFORMER WITH THE SYMMETRY-RELATED COUNTERPART. THE FOLLOWING WATERS WERE USED TO ACCOUNT FOR DENSITY DUE TO THIS CONFORMER OF TYR B 22: HOH 519, HOH 1239.
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Refinement step | Cycle: LAST / Resolution: 1.5→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.57 Å / % reflection obs: 34.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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