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Open data
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Basic information
Entry | Database: PDB / ID: 2izf | |||||||||
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Title | STREPTAVIDIN-BIOTIN PH 4.0 I222 COMPLEX | |||||||||
![]() | STREPTAVIDIN | |||||||||
![]() | BIOTIN-BINDING PROTEIN / STREPTAVIDIN-BIOTIN | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Katz, B.A. | |||||||||
![]() | ![]() Title: Binding of biotin to streptavidin stabilizes intersubunit salt bridges between Asp61 and His87 at low pH. Authors: Katz, B.A. #1: ![]() 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. #2: ![]() 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. #3: ![]() Title: Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design Authors: Katz, B.A. #4: ![]() Title: Topochemical catalysis achieved by structure-based ligand design. Authors: Katz, B.A. / Cass, R.T. / Liu, B. / Arze, R. / Collins, N. #5: ![]() 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: ![]() Title: Structure-Based Design of High Affinity Streptavidin Binding Ligands Containing Thioether Crosslinks Authors: Katz, B.A. / Johnson, C.R. / Cass, R.T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.6 KB | Display | ![]() |
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PDB format | ![]() | 63 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.8 KB | Display | ![]() |
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Full document | ![]() | 456.8 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2izaC ![]() 2izbC ![]() 2izcC ![]() 2izdC ![]() 2izeC ![]() 2izgC ![]() 2izhC ![]() 2iziC ![]() 2izjC ![]() 2izkC ![]() 2izlC ![]() 2rtaC ![]() 2rtbC ![]() 2rtcC ![]() 2rtdC ![]() 2rteC ![]() 2rtfC ![]() 2rtgC ![]() 2rthC ![]() 2rtiC ![]() 2rtjC ![]() 2rtkC ![]() 2rtlC ![]() 2rtmC ![]() 2rtnC ![]() 2rtoC ![]() 2rtpC ![]() 2rtqC ![]() 2rtrC C: citing same article ( |
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Similar structure data |
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Links
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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: (-0.999739, -0.020722, -0.009639), Vector: |
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Components
#1: Protein | Mass: 12965.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 19.8 % Description: REJECTION CRITERIA: (I(H)I - ) > [0.30 * () + 0.10*I(H)I], WHERE I(H)I IS THE ITH OBSERVATION OF THE INTENSITY OF REFLECTION H (M.G.ROSSMANN ET AL., J.APPL.CRYST. 12, 570-581). THIS ...Description: REJECTION CRITERIA: (I(H)I - ) > [0.30 * ( | ||||||||||||||||||||
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Crystal grow | pH: 4 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 4.0. | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
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 | Ambient temp details: ROOM |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Details: MSC MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 28476 / Observed criterion σ(I): 0.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.044 |
Reflection | *PLUS Highest resolution: 1.58 Å / Num. measured all: 91953 |
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Processing
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Refinement | Resolution: 1.58→7.5 Å / Cross valid method: FREE R / σ(F): 1.9 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B13, GLU B14, ALA B15, (CG, CD, OE1, OE2 OF GLU B51), (NE, CZ, NH1, NH2 OF ARG B53), ASP B67, GLY B68 (NE, CZ, NH1, NH2 ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B13, GLU B14, ALA B15, (CG, CD, OE1, OE2 OF GLU B51), (NE, CZ, NH1, NH2 OF ARG B53), ASP B67, GLY B68 (NE, CZ, NH1, NH2 OF ARG B84), (NE, CZ, NH1, NH2 OF ARG B103), (CG, CD, OE1, OE2 OF GLU B116), (MAIN CHAIN OF LYS B134), (CB, CG, CD, CE OF LYS B134), (NZ OF LYS B134), PRO B135, ALA D13, GLU D14, ALA D15, (CG, OD1, OD2 OF ASP D36), (NE, CZ, NH1, NH2 OF ARG D53), (CG, OD1, ND2 OF ASN D82), (NE, CZ, NH1, NH2 OF ARG D84), (CG, CD, OE1, OE2 OF GLU D101), (NE, CZ, NH1, NH2 OF ARG D103), (CG, CD, OE1, OE2 OF GLU D116), IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS INVOLVING THE ABOVE WATERS. BULK SOLVENT CONTRIBUTIONS WERE INCLUDED IN REFINEMENT.
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Refinement step | Cycle: LAST / Resolution: 1.58→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.64 Å / % reflection obs: 41.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.166 |