+Open data
-Basic information
Entry | Database: PDB / ID: 2izk | |||||||||
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Title | STREPTAVIDIN-GLYCOLURIL PH 2.58 I4122 COMPLEX | |||||||||
Components | STREPTAVIDIN | |||||||||
Keywords | BIOTIN-BINDING PROTEIN / STREPTAVIDIN-SMALL MOLECULE LIGAND / DESIGNED SMALL MOLECULE LIGAND WITH MICROMOLAR AFFINITY | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces avidinii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.3 Å | |||||||||
Authors | Katz, B.A. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Binding of biotin to streptavidin stabilizes intersubunit salt bridges between Asp61 and His87 at low pH. Authors: Katz, B.A. #1: 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. #2: 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. #3: Journal: J.Am.Chem.Soc. / Year: 1996 Title: Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design Authors: Katz, B.A. #4: Journal: J.Biol.Chem. / Year: 1995 Title: Topochemical Catalysis Achieved by Structure-Based Design Authors: Katz, B.A. / Cass, R.T. / Liu, B. / Arze, R. / Collins, N. #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 Ligands Containing Thioether Crosslinks 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 | 2izk.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2izk.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 2izk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2izk_validation.pdf.gz | 448 KB | Display | wwPDB validaton report |
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Full document | 2izk_full_validation.pdf.gz | 454.5 KB | Display | |
Data in XML | 2izk_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 2izk_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/2izk ftp://data.pdbj.org/pub/pdb/validation_reports/iz/2izk | HTTPS FTP |
-Related structure data
Related structure data | 2izaC 2izbC 2izcC 2izdC 2izeC 2izfC 2izgC 2izhC 2iziC 2izjC 2izlC 2rtaC 2rtbC 2rtcC 2rtdC 2rteC 2rtfC 2rtgC 2rthC 2rtiC 2rtjC 2rtkC 2rtlC 2rtmC 2rtnC 2rtoC 2rtpC 2rtqC 2rtrC 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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-Components
#1: Protein | Mass: 12965.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629 |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-GLL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 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: 2.58 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25% 1.0M POTASSIUM ACETATE ADJUSTED TO PH 2.58. 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: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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: 24284 / Redundancy: 4.1 % / Rmerge(I) obs: 0.058 |
Reflection | *PLUS Highest resolution: 1.32 Å / Num. measured all: 99961 |
-Processing
Software |
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Refinement | Highest resolution: 1.3 Å / Cross valid method: FREE R / σ(F): 1 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA13, GLU14, ALA15, (SIDE CHAIN OF ALA35), (CG, OD1, AND OD2 OF ASP36), (CG, HG1, HG2, CD, OE1, OE2 OF GLU44), (CA AND HA1 ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA13, GLU14, ALA15, (SIDE CHAIN OF ALA35), (CG, OD1, AND OD2 OF ASP36), (CG, HG1, HG2, CD, OE1, OE2 OF GLU44), (CA AND HA1 AND HA2 OF GLY48), (SIDE CHAIN OF ASN49), (SIDE CAHIN OF ALA50) (CG, HG1, HG2, CD, OE1, OE2 OF GLU51), (TERMINUS OF ARG53), (CG, HG1, HG2 OF ARG84), (CD, HD1, HD2, NE, HE, CZ NH1, HH11, HH12, NH2, HH21, HH22 OF ARG84), (CB, HB1, HB2, HB3 OF ALA100), (CG, HG1, HG2, CD, OE1, OE2 OF GLU101), (TERMINUS OF ARG103), (CD, OE1, OE2 OF GLU116), (CE, HE1, HE2 OF LYS121), (NZ, HZ1, HZ2, HZ3 OF LYS121), (CB, HB1, HB2, CG, HG1, HG2, CD, HD1, HD2) OF LYS134, (CE, HE1, HE2, NZ, HZ1, HZ2, HZ3 OF LYS134), PRO135. 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 / Highest resolution: 1.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.57 Å / % reflection obs: 23.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.178 |