+Open data
-Basic information
Entry | Database: PDB / ID: 2iza | |||||||||
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Title | APOSTREPTAVIDIN PH 2.00 I4122 STRUCTURE | |||||||||
Components | STREPTAVIDIN | |||||||||
Keywords | BIOTIN-BINDING PROTEIN / APOSTREPTAVIDIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces avidinii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.46 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 to 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 | 2iza.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iza.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 2iza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/2iza ftp://data.pdbj.org/pub/pdb/validation_reports/iz/2iza | HTTPS FTP |
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-Related structure data
Related structure data | 2izbC 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 (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: 12738.730 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-FMT / |
#3: 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: 2.87 Å3/Da / Density % sol: 40 % 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 Details: SYNTHETIC MOTHER LIQUOR = 75% SATURATED AMMONIUM SULFATE, 25 % 1.0 M SODIUM FORMATE ADJUSTED TO PH 2.00. 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: 31893 / Redundancy: 6.6 % / Rmerge(I) obs: 0.074 |
Reflection | *PLUS Highest resolution: 1.32 Å / Num. measured all: 211479 |
-Processing
Software |
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Refinement | Resolution: 1.46→7.5 Å / Cross valid method: FREE R / σ(F): 1.7 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA13, GLU14, (ALA15 (EXCEPT FOR C AND O)), (MAIN CHAIN OF GLN24), (SIDE CHAIN OF GLN24), (MAIN CHAIN OF LEU25), (SIDE ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA13, GLU14, (ALA15 (EXCEPT FOR C AND O)), (MAIN CHAIN OF GLN24), (SIDE CHAIN OF GLN24), (MAIN CHAIN OF LEU25), (SIDE CHAIN OF LEU25), GLY26, (MAIN CHAIN OF ALA35) ALA35), (SIDE CHAIN OF ALA35), (N, HN, CA, HA, C, O, CB, HB1, HB2 OF ASP36), (CG, OD1, AND OD2 OF ASP36), (CG, HG1, HG2, CD, OE1, OE2 OF GLU44), (MAIN CHAIN OF SER45), (SIDE CHAIN OF SER45), (H, HN OF ALA46), (CA, HA, C, O, CB, HB1, HB2, HB3 OF ALA46), VAL47, GLY48, ASN49, ALA50, GLU51, (SIDE CHAIN OF SER52), (CD, HD1, HD2 OF ARG53), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG53), PRO64, ALA65, THR66, ASP67, GLY68, (CG, HG1, HG2 OF ARG84), (CD, HD1, HD2, NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG84), GLY99, ALA100, (N, HN, 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), (MAIN CHAIN OF ALA117), (SIDE CHAIN OF ALA117), (CG, HG1, HG2, CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1, HZ2, HZ3 OF LYS121), (CE, HE1, HE2, NZ, HZ1, HZ2, HZ3 OF LYS132).
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Refinement step | Cycle: LAST / Resolution: 1.46→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.53 Å / % reflection obs: 41.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.21 / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.21 |