+Open data
-Basic information
Entry | Database: PDB / ID: 2izd | |||||||||
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Title | APOSTREPTAVIDIN pH 3.0 I222 COMPLEX | |||||||||
Components | STREPTAVIDIN | |||||||||
Keywords | BIOTIN-BINDING PROTEIN / APOSTREPTAVIDIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces avidinii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 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 ligand 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 | 2izd.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2izd.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 2izd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/2izd ftp://data.pdbj.org/pub/pdb/validation_reports/iz/2izd | HTTPS FTP |
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-Related structure data
Related structure data | 2izaC 2izbC 2izcC 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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: (-0.999699, -0.022536, -0.009715), Vector: |
-Components
-Protein , 1 types, 2 molecules BD
#1: Protein | Mass: 12965.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629 |
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-Non-polymers , 5 types, 147 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-IOD / | #5: Chemical | ChemComp-NH4 / | #6: 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: 2.28 Å3/Da / Density % sol: 46.14 % 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 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 3.0. | ||||||||||||||||||||
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: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 | Resolution: 1.6→7.5 Å / Num. obs: 40359 / Redundancy: 2.5 % / Rmerge(I) obs: 0.083 |
Reflection | *PLUS Highest resolution: 1.31 Å / Num. measured all: 99140 |
-Processing
Software |
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Refinement | Resolution: 1.6→7.5 Å / Cross valid method: FREE R / σ(F): 2.5 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B13, B14, B15, (CG, HG1, HG2, CD, OE1, OE2 OF GLU B51), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B53), SER B62, ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B13, B14, B15, (CG, HG1, HG2, CD, OE1, OE2 OF GLU B51), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B53), SER B62, ALA B63, PRO B64, ALA B65, THR B66, ASP B67, GLY B68 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B84), (SIDE CHAIN OF HIS B87), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B103), (CG, HG1, HG2, CD, OE1, OE2 OF GLU B116), (CB, HB1, HB2, CG, HG1, HG2 OF LYS B134), (CD, HD1, HD2 OF LYS B134), PRO B135, ALA D13, (N, HN, CA, HA, CB, HB1, HB2, C, O OF GLU D14), (CG, HG1, HG2, CD, OE1, OE2 OF GLU D14), ALA D15 (CG, OD1, OD2 OF ASP D36), (OG AND HG1 OF SER D45), ALA D46, VAL D47, GLY D48, ASN D49, ALA D50, (GLU D51, EXCEPT C AND O) (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), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG D103), (CG, HG1, HG2, CD, OE1, OE2 OF GLU D116). RESIDUES TYR B60 THROUGH SER B69 AND TYR D60 THROUGH SER D69 WERE REFINED IN TWO CONFORMATIONS BECAUSE UPON PROTONATION OF ASP61 AT LOW PH, ASP61 UNDERGOES A LARGE SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE LOOPS COMRISING RESIDUES ASP B61 THROUGH SER B69 AND ASP D61 THROUGH SER D69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. TYR B22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A 2 - FOLD RELATED TYR 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: HOH491, AND HOH1460. IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS INVOLVING HOH491, HOH1460.
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Refinement step | Cycle: LAST / Resolution: 1.6→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 Å / % reflection obs: 29.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.76 Å / Rfactor obs: 0.208 |