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Open data
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Basic information
Entry | Database: PDB / ID: 2izb | |||||||||
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Title | APOSTREPTAVIDIN PH 3.12 I4122 STRUCTURE | |||||||||
![]() | STREPTAVIDIN | |||||||||
![]() | BIOTIN-BINDING PROTEIN / APOSTREPTAVIDIN | |||||||||
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 to 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 | ![]() | 66.2 KB | Display | ![]() |
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PDB format | ![]() | 51.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.3 KB | Display | ![]() |
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Full document | ![]() | 441.6 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2izaC ![]() 2izcC ![]() 2izdC ![]() 2izeC ![]() 2izfC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12867.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-FMT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 34.7 % 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: 3.12 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M SODIUM ACETATE ADJUSTED TO PH 3.12. 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: 28447 / Redundancy: 5.4 % / Rmerge(I) obs: 0.082 |
Reflection | *PLUS Highest resolution: 1.24 Å / Num. measured all: 154360 |
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Processing
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Refinement | Resolution: 1.2→7.5 Å / Cross valid method: FREE R / σ(F): 1.8 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA13, GLU14, ALA15, (MAIN CHAIN OF GLN24), (SIDE CHAIN OF GLN24), (MAIN CHAIN OF LEU25), (SIDE CHAIN OF LEU25), GLY26, ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA13, GLU14, ALA15, (MAIN CHAIN OF GLN24), (SIDE CHAIN OF GLN24), (MAIN CHAIN OF LEU25), (SIDE CHAIN OF LEU25), GLY26, (SIDE CHAIN OF ALA35), (CG, OD1, AND OD2 OF ASP36), (CG, HG1, HG2, CD, OE1, OE2 OF GLU44), ALA46, VAL47, GLY48, ASN49, ALA50, GLU51, (SIDE CHAIN OF SER52), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG53), (CG, HG1, HG2 OF ARG84), (CD, HD1, HD2, NE, HE, CZ NH1, HH11, HH12, NH2, HH21, HH22 OF ARG84), GLY99, (MAIN CHAIN OF ALA100), (CB, HB1, HB2, HB3 OF ALA100), (N, HN OF GLU101), (CA, HA, CB, HB1, HB2 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), (ALA117), (SIDE CHAIN OF ASN118), (CG, HG1, HG2, CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1, HZ2, HZ3 OF LYS121), (CE, HE1, HE2, NZ, HZ1, HZ2, HZ3 OF LYS132), (CE, HE1, HE2, NZ, HZ1, HZ2, HZ3 OF LYS134). RESIDUES 60 - 69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP61 AT LOW PH, ASP61 UNDERGOES A LARGE SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE LOOP COMRISING RESIDUES 61 - 69 ALSO UNDERGOES CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION.
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Refinement step | Cycle: LAST / Resolution: 1.2→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.48 Å / % reflection obs: 41.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.207 |