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Yorodumi- PDB-1vwf: STREPTAVIDIN COMPLEXED WITH CYCLO-AC-[CHPQGPPC]-NH2 MONOMER, PH 3.67 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vwf | ||||||
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Title | STREPTAVIDIN COMPLEXED WITH CYCLO-AC-[CHPQGPPC]-NH2 MONOMER, PH 3.67 | ||||||
Components |
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Keywords | COMPLEX (BIOTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) / CYCLIC PEPTIDE DISCOVERED BY PHAGE DISPLAY / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.92 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 | 1vwf.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vwf.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/1vwf ftp://data.pdbj.org/pub/pdb/validation_reports/vw/1vwf | HTTPS FTP |
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-Related structure data
Related structure data | 1vwaC 1vwbC 1vwcC 1vwdC 1vweC 1vwgC 1vwhC 1vwiC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12965.025 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / References: UniProt: P22629 |
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#2: Protein/peptide | Mass: 863.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 34.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.67 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 3.67. | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4.5 / 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: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 12118 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 |
Reflection | *PLUS Highest resolution: 1.84 Å / Num. measured all: 38381 / Rmerge(I) obs: 0.08 |
-Processing
Software |
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Refinement | Resolution: 1.92→7.5 Å / σ(F): 2 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, (MAIN CHAIN OF GLN 24), (SIDE CHAIN OF GLN 24),(MAIN CHAIN OF LEU 25), (SIDE CHAIN OF LEU 25), GLY 26, (CG, ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, (MAIN CHAIN OF GLN 24), (SIDE CHAIN OF GLN 24),(MAIN CHAIN OF LEU 25), (SIDE CHAIN OF LEU 25), GLY 26, (CG, OD1, OD2 OF ASP 36), (N, CA OF ALA 46), (CB, C, O OF ALA 46), VAL 47, GLY 48, ASN 49, ALA 50, SIDE CHAIN OF GLU 51, TERMINUS OF ARG 53, GLY 99, ALA 100, (CG, CD, OE1, OE2 OF GLU 101), TERMINUS OF ARG 103, (CE, NZ OF LYS 121), (ACE P 0 AND CYS P 1), PRO P 7, (CYS P 8 AND NH2 P 9).
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Refinement step | Cycle: LAST / Resolution: 1.92→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.95 Å / % reflection obs: 36.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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