+Open data
-Basic information
Entry | Database: PDB / ID: 2rtb | |||||||||
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Title | APOSTREPTAVIDIN, PH 3.32, SPACE GROUP I222 | |||||||||
Components | STREPTAVIDIN | |||||||||
Keywords | BIOTIN-BINDING PROTEIN / APOSTREPTAVIDIN / PH 3.32 | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces avidinii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.5 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: Chem.Biol. / Year: 1995 Title: Topochemistry for Preparing Ligands that Dimerize Receptors Authors: Katz, B.A. / Stroud, R.M. / Collins, N. / Liu, B. / Arze, R. #6: 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. #7: Journal: J.Am.Chem.Soc. / Year: 1995 Title: Structure-Based Design of High Affinity Streptavidin Binding Cyclic Peptide Ligands Containing Thioether Cross-Links 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 | 2rtb.cif.gz | 113.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rtb.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 2rtb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rtb_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 2rtb_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 2rtb_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 2rtb_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/2rtb ftp://data.pdbj.org/pub/pdb/validation_reports/rt/2rtb | HTTPS FTP |
-Related structure data
Related structure data | 2izaC 2izbC 2izcC 2izdC 2izeC 2izfC 2izgC 2izhC 2iziC 2izjC 2izkC 2izlC 2rtaC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999717, -0.022583, -0.007445), Vector: |
-Components
#1: Protein | Mass: 14181.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629 #2: Chemical | ChemComp-NA / | #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 22.3 % 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, A.G.W.LESLIE, S.S.ABDEL-MEGUID, T.TSUKIHARA, ...Description: REJECTION CRITERIA: (I(H)I - ) > [0.30 * ( | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.32 Details: SYNTHETIC MOTHER LIQUOR OF 75% SATURATED AMMONIUM SULFATE, 25% 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 3.32. | ||||||||||||||||||||||||||||||
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 | Mean temperature: 273 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 34070 / Redundancy: 2.3 % / Rmerge(I) obs: 0.061 |
Reflection | *PLUS Highest resolution: 1.33 Å / Num. measured all: 78208 |
-Processing
Software |
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Refinement | Resolution: 1.5→7.5 Å / σ(F): 2.7 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B 13 GLU B 14 ALA B 15 GLU B 51 (CG, HG1, HG2, CD, OE1, OE2) ARG B 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B 13 GLU B 14 ALA B 15 GLU B 51 (CG, HG1, HG2, CD, OE1, OE2) ARG B 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ARG B 84 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLY B 98 GLY B 99 ALA B 100 GLU B 101 ALA B 102 ARG B 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU B 116 (CG, HG1, HG2, CD, OE1, OE2) LYS B 134 PRO B 135 ALA D 13 GLU D 14 ALA D 15 ASP D 36 (CG, OD1, OD2) ARG D 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ASN D 82 (CG, OD1, ND2, HD21, HD22) ARG D 84 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ALA D 100 GLU D 101 (CB, HB1, HB2, CG, HG1, HG2, CD, OE1, OE2) ARG D 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU D 116 (CG, HG1, HG2, CD, OE1, OE2) VAL D 133 RESIDUES TYR B 60 THROUGH SER B 69 AND TYR D 60 THROUGH SER D 69 WERE REFINED IN TWO CONFORMATIONS BECAUSE UPON PROTONATION OF ASP 61 AT LOW PH, ASP 61 UNDERGOES A LARGE SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE LOOPS COMPRISING RESIDUES ASP B 61 THROUGH SER B 69 AND ASP D 61 THROUGH SER D 69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. TYR B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A 2-FOLD RELATED B 22. 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 B 22: HOH 491, HOH 1460. NO HYDROGENS ARE INCLUDED FOR THESE "WATERS".
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Refinement step | Cycle: LAST / Resolution: 1.5→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.57 Å / % reflection obs: 49.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.209 |