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Open data
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Basic information
Entry | Database: PDB / ID: 2izj | ||||||
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Title | STREPTAVIDIN-BIOTIN PH 3.50 I4122 STRUCTURE | ||||||
![]() | 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 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 | ![]() | 62.6 KB | Display | ![]() |
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PDB format | ![]() | 47.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434 KB | Display | ![]() |
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Full document | ![]() | 438.6 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2izaC ![]() 2izbC ![]() 2izcC ![]() 2izdC ![]() 2izeC ![]() 2izfC ![]() 2izgC ![]() 2izhC ![]() 2iziC ![]() 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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Components
#1: Protein | Mass: 12965.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-BTN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 37.7 % 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: 3.5 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 3.50. COMPLEX PRODUCED BY SOAKING STREPTAVIDIN-2-IMINOBIOTIN CO-CRYSTAL. | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
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 | Ambient temp details: ROOM |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / 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: 25529 / Redundancy: 1.9 % / Rmerge(I) obs: 0.095 |
Reflection | *PLUS Highest resolution: 1.32 Å / Num. measured all: 46433 |
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Processing
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Refinement | Highest resolution: 1.3 Å / Cross valid method: FREE R / σ(F): 1.2 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA13, GLU14, ALA15, (SIDE CHAIN OF ALA35), (N, HN, CA, HA, CB, HB1, HB2, C, O OF ASP36), (CG, OD1, AND OD2 OF ASP36), (NE, ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA13, GLU14, ALA15, (SIDE CHAIN OF ALA35), (N, HN, CA, HA, CB, HB1, HB2, C, O OF ASP36), (CG, OD1, AND OD2 OF ASP36), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG53), GLY99, (MAIN CHAIN OF ALA100), (CB, HB1, HB2, HB3 OF ALA100), (N, HN, CA, HA, CB, HB1, HB2, C, O OF GLU101 (CG, HG1, HG2, CD, OE1, OE2 OF GLU101), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG103), (N, HN, CA, HA, CB, HB1, HB2, CG, HG1, HG2, C, O OF GLU116), (CD, OE1, OE2 OF GLU116), (SIDE CHAIN OF ALA117), (SIDE CHAIN OF ASN118), (CG, HG1, HG2, CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1, HZ2, HZ3 OF LYS121), (CB, HB1, HB2, CG, HG1, HG2, CD, HD1, HD2 OF LYS134), (NZ, HZ1, HZ2, HZ3 OF LYS134).
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Refinement step | Cycle: LAST / Highest resolution: 1.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.43→1.49 Å / % reflection obs: 39.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.206 |