+Open data
-Basic information
Entry | Database: PDB / ID: 1vwe | ||||||
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Title | STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 3.6 | ||||||
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: 1.5 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 | 1vwe.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vwe.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/1vwe ftp://data.pdbj.org/pub/pdb/validation_reports/vw/1vwe | HTTPS FTP |
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-Related structure data
Related structure data | 1vwaC 1vwbC 1vwcC 1vwdC 1vwfC 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
#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: 758.911 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: 2.79 Å3/Da / Density % sol: 35.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.6 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 3.6. | |||||||||||||||||||||||||||||||||||||||||||||||||
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: 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: 26406 / Redundancy: 4.8 % / Rmerge(I) obs: 0.081 |
Reflection | *PLUS Highest resolution: 1.33 Å / Num. measured all: 126387 |
-Processing
Software |
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Refinement | Resolution: 1.5→7.5 Å / σ(F): 2.7 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, 26, 35, MAIN CHAIN AND ...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, 26, 35, MAIN CHAIN AND CB, HB1, HB2 OF ASP 36, CG, OD1, AND OD2 OF ASP 36, 46, 47, 48, 49, 50, 51 (EXCEPT C AND O), SIDE CHAIN OF SER 52, TERMINUS OF ARG 53, ARG 84 SIDE CHAIN FROM CB OUTWARD, 99, 100, SIDE CHAIN OF GLU 101 FROM CG OUTWARD, TERMINUS OF ARG 103, GLN 116 SIDE CHAIN, 117 MAIN CHAIN, 117 SIDE CHAIN, LYS 121 FROM CG OUTWARD, LYS 132 SIDE CHAIN. DISCRETELY DISORDERED ENTIRE RESIDUES WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, (ACE P 0 AND CYS P 1), (CYS P 6 AND NH2 P 7). DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: HIS 87, GLN 107. RESIDUES 60 - 69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF AS P61 AT LOW PH, ASP 61 UNDERGOES A LARGE SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE LOOP COMPRISING RESIDUES 61 - 69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. DISORDERED WATERS ARE HOH 142 WHICH OCCUPIES THE SPACE AVAILABLE WHEN ASP 61 IS IN CONFORMATION NO. 1; HOH 279, HOH 305, AND HOH 313 WHICH ARE CLOSE TO SYMMETRY-RELATED EQUIVALENTS OF THEMSELVES, RESPECTIVELY. NO ENERGY INTERACTIONS INVOLVING HOH 279, HOH 305 OR HOH 313 WERE TURNED ON DURING REFINEMENT. 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, 26, 35, MAIN CHAIN AND CB, HB1, HB2 OF ASP 36, CG, OD1, AND OD2 OF ASP 36, 46, 47, 48, 49, 50, 51 (EXCEPT C AND O), SIDE CHAIN OF SER 52, TERMINUS OF ARG 53, ARG 84 SIDE CHAIN FROM CB OUTWARD, 99, 100, SIDE CHAIN OF GLU 101 FROM CG OUTWARD, TERMINUS OF ARG 103, GLN 116 SIDE CHAIN, 117 MAIN CHAIN, 117 SIDE CHAIN, LYS 121 FROM CG OUTWARD, LYS 132 SIDE CHAIN.
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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: 32.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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