+Open data
-Basic information
Entry | Database: PDB / ID: 1vwa | |||||||||
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Title | STREPTAVIDIN-FSHPQNT | |||||||||
Components |
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Keywords | COMPLEX (BIOTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) / LINEAR 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: 1.85 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 | 1vwa.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vwa.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vwa_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 1vwa_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | 1vwa_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 1vwa_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/1vwa ftp://data.pdbj.org/pub/pdb/validation_reports/vw/1vwa | HTTPS FTP |
-Related structure data
Related structure data | 1vwbC 1vwcC 1vwdC 1vweC 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999757, -0.021401, -0.005364), 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: 830.864 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
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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: 2.29 Å3/Da / Density % sol: 22 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4 Details: SYNTHETIC MOTHER LIQUOR = 50 % SATURATED AMMONIUM SULFATE, 50 % 0.1 M POTASSIUM ACETATE., pH 4.0 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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 / 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: 25792 / Redundancy: 3.8 % / Rmerge(I) obs: 0.083 |
Reflection | *PLUS Highest resolution: 1.63 Å / Num. measured all: 98073 |
-Processing
Software |
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Refinement | Resolution: 1.85→7.5 Å / σ(F): 2 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 47, B 48, B 49, B 50, TERMINUS OF ARG B 53, B 67, B 68, TERMINUS OF ARG B 84, TERMINUS OF ARG B 103, ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 47, B 48, B 49, B 50, TERMINUS OF ARG B 53, B 67, B 68, TERMINUS OF ARG B 84, TERMINUS OF ARG B 103, TERMINUS OF GLU B 116, B 135, D 13, D 14, D 15, D 46, D 47, D 48, D 49, D 50, D 51, (TERMINUS OF ARG D 84), (TERMINUS OF ARG D 103), PEPTIDE RESIDUES M 2, M 7. M 1 WAS NOT LOCATED OR INCLUDED IN THE MODEL. DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED WERE B 22, D 73, D 107, AND P 1. 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 585, HOH 1056. IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS BETWEEN THESE WATERS AND THE REST OF THE STRUCTURE. HOH 1118 IS CLOSE TO ITS SYMMETRY-RELATED EQUIVALENT AND IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS BETWEEN THIS WATER AND THE REST OF THE STRUCTURE. BULK SOLVENT WAS REFINED. HOH 1095 OCCUPIES A PORTION OF SPACE THE SAME AS CONFORMER 2 OF B 22. HOH 595 IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 1122. THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 47, B 48, B 49, B 50, TERMINUS OF ARG B 53, B 67, B 68, TERMINUS OF ARG B 84, TERMINUS OF ARG B 103, TERMINUS OF GLU B 116, B 135, D 13, D 14, D 15, D 46, D 47, D 48, D 49, D 50, D 51, (TERMINUS OF ARG D 84), (TERMINUS OF ARG D 103), PEPTIDE RESIDUES M 2, M 7. M 1 WAS NOT LOCATED OR INCLUDED IN THE MODEL. 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 585, HOH 1056. IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS BETWEEN THESE WATERS AND THE REST OF THE STRUCTURE. HOH 1118 IS CLOSE TO ITS SYMMETRY-RELATED EQUIVALENT AND IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS BETWEEN THIS WATER AND THE REST OF THE STRUCTURE. BULK SOLVENT WAS REFINED. HOH 1095 OCCUPIES A PORTION OF SPACE THE SAME AS CONFORMER 2 OF B 22. HOH 595 IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 1122.
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Refinement step | Cycle: LAST / Resolution: 1.85→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.93 Å / % reflection obs: 42 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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