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Yorodumi- PDB-1vwl: STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 3.5, I222 COMPLEX -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vwl | |||||||||
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Title | STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 3.5, 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) Bothrops insularis (golden lancehead) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.45 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 | 1vwl.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vwl.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 1vwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/1vwl ftp://data.pdbj.org/pub/pdb/validation_reports/vw/1vwl | HTTPS FTP |
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-Related structure data
Related structure data | 1vwaC 1vwbC 1vwcC 1vwdC 1vweC 1vwfC 1vwgC 1vwhC 1vwiC 1vwjC 1vwkC 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: (-0.99989, -0.01486, 0.002413), 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 natural source / Source: (natural) Bothrops insularis (golden lancehead) #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: 2.16 Å3/Da / Density % sol: 18.1 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.5 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 3.5. | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Pahler, A., (1987) J. Biol. Chem., 262, 13933. / pH: 4 | ||||||||||||||||||||||||||||||||||||
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 / 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: 42836 / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 |
Reflection | *PLUS Highest resolution: 1.32 Å / Num. measured all: 79817 / Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Resolution: 1.45→7.5 Å / σ(F): 1.7 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), (TERMINUS OF ARG B 84) ...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), (TERMINUS OF ARG B 84), (SIDE CHAIN OF GLU B 101), (TERMINUS OF ARG B 103), (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), (TERMINUS OF ARG D 84), (TERMINUS OF ARG D 103), (M 9 AND M 10), (P 9 AND P 10). DISCRETELY DISORDERED ENTIRE RESIDUES WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: B 60, B 61, B 62, B 63, B 64, B 65, B 66, B 67, B 68, B 69, D 61, D 62, D 63, D 64, D 65, D 66, D 67, D 68, D 69, (ACE P 0 AND CYS P 1), (CYS P 6 AND NH2 P 7). RESIDUES B 60 - B 69 AND D 60 - D 69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP 61 AT LOW PH, ASP B 61 AND ASP D 61 UNDERGO LARGE SHIFTS IN CONFORMATION AND CHANGES IN HYDROGEN BONDING. THE LOOPS COMPRISING RESIDUES B 61 - B 69 AND D 61 - D 69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED WERE B 29, B 40, B 42, B 73, B 110, D 32, D 87, D 107, D 110. 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 516, HOH 519, HOH 1249. DISORDERED WATERS ARE HOH 852 AND HOH 1414 WHICH ARE CLOSE TO SYMMETRY-RELATED EQUIVALENTS OF THEMSELVES, RESPECTIVELY; HOH 1284 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF AND OCCUPIES THE SPACE AVAILABLE WHEN ASN D 107 IS IN ONE OF ITS DISCRETE CONFORMATIONS. HOH 624 WHICH IS CLOSE TO HOH 1182; HOH 504 WHICH IS CLOSE TO HOH 1403; HOH 505 WHICH IS CLOSE TO HOH 1390; HOH 727 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 1365; HOH 1180 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 1414; HOH 1139 THAT OCCUPIES THE REGION OF SPACE AVAILABLE WHEN ASP B 61 IS IN CONFORMATION NO. 2; HOH 1167 THAT OCCUPIES THE REGION OF SPACE AVAILABLE WHEN ASP D 61 IS IN CONFORMATION NO. 2; HOH 1358 WHICH MAKES A H-BOND WITH OG2 OF THR D 32 IN CONFORMATION 1; HOH 513 WHICH IS CLOSE TO MAIN CHAIN CARBONYL OF B 49; HOH 514 WHICH IS CLOSE TO CA OF B 51; HOH 1251 WHICH IS CLOSE TO O OF B 51; HOH 1209 WHICH IS CLOSE TO CA OF B 48; HOH 1375 WHICH IS CLOSE TO O OF D 51. IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS INVOLVING HOH 513, HOH 514, HOH 516, HOH 519, HOH 852, HOH 1249, HOH 1251, HOH 1375, HOH 1284, HOH 1414. DISULFIDE BOND OF PHAGE-DISCOVERED PEPTIDE IS REPLACED WITH THIOETHER. 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), (TERMINUS OF ARG B 84), (SIDE CHAIN OF GLU B 101), (TERMINUS OF ARG B 103), (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), (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 516, HOH 519, HOH 1249.
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Refinement step | Cycle: LAST / Resolution: 1.45→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.52 Å / % reflection obs: 32.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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