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Open data
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Basic information
Entry | Database: PDB / ID: 2izh | |||||||||
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Title | STREPTAVIDIN-BIOTIN PH 10.44 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 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 | ![]() | 115 KB | Display | ![]() |
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PDB format | ![]() | 91.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 452.9 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2izaC ![]() 2izbC ![]() 2izcC ![]() 2izdC ![]() 2izeC ![]() 2izfC ![]() 2izgC ![]() 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: (-0.999565, -0.028348, -0.008168), 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: 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: 20.7 % 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: 10.44 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 50.0 MM CAPS ADJUSTED TO PH 10.44. | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4 / 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: 43615 / Redundancy: 2 % / Rmerge(I) obs: 0.054 |
Reflection | *PLUS Highest resolution: 1.33 Å / Num. measured all: 88975 |
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Processing
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Refinement | Resolution: 1.36→7.5 Å / Cross valid method: FREE R / σ(F): 0.5 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA_B13, GLU_B14, ALA_B15, SIDE CHAIN OF TYR_B22, (CG, HG1, HG2, CD, OE1, OE2 OF GLU_B51), (NE, HE, CZ, NH1, HH11, HH12, ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA_B13, GLU_B14, ALA_B15, SIDE CHAIN OF TYR_B22, (CG, HG1, HG2, CD, OE1, OE2 OF GLU_B51), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG_B53), ASP_B67, (CA, HA1, HA2 OF GLY_B68), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG_B84), (CG, HG1, HG2, CD, OE1, OE2 OF GLU_B101), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG_B103), (CG, HG1, HG2, CD, OE1, OE2 OF GLU_B116), (CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1, HZ2, HZ3, C, OT1, OT2 OF LYS B134), (N, HT1, HT2, HT3, CA, HA, C, O OF ALA_D13), GLU_D14, ALA_D15 (CG, OD1, OD2 OF ASP_D36), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG_D53), (CG, OD1, ND2, HD21, HD22 OF ASN_D82), (CG AND OUTWARD OF TYR_D83), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG_D84), (CG, HG1, HG2, CD, OE1, OE2 OF GLU_D101), (CB, HB1, HB2, CG, HG1, HG2, CD, OE1, OE2 OF GLU D116), (CD, HD1, HD2, CE, HE1, HE2, NZ, NZ1, NZ2, NZ3 OF LYS_D134), (C, OT1, OT2 OF LYS_D134). B22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A 2 - FOLD RELATED B22. PROPER REFINEMENT WITH XPLOR 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 B22: HOH1637, HOH1777, HOH1778.
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Refinement step | Cycle: LAST / Resolution: 1.36→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.42 Å / % reflection obs: 30.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.189 |