+Open data
-Basic information
Entry | Database: PDB / ID: 2rtr | ||||||
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Title | STREPTAVIDIN-2-IMINOBIOTIN COMPLEX, PH 4.0, SPACE GROUP I222 | ||||||
Components | STREPTAVIDIN | ||||||
Keywords | BIOTIN-BINDING PROTEIN / STREPTAVIDIN-2-IMINOBIOTIN / PH 4.0 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.62 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 | 2rtr.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rtr.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 2rtr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rtr_validation.pdf.gz | 419.6 KB | Display | wwPDB validaton report |
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Full document | 2rtr_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 2rtr_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 2rtr_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/2rtr ftp://data.pdbj.org/pub/pdb/validation_reports/rt/2rtr | HTTPS FTP |
-Related structure data
Related structure data | 2izaC 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 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99982, -0.01814, -0.005621), 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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 23.7 % 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, 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: 4 Details: ROOM TEMPERATURE, PH 4.00. SYNTHETIC MOTHER LIQUOR OF 75% SATURATED AMMONIUM SULFATE, 25% 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 4.0. | ||||||||||||||||||||||||||||||
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 source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU / 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: 28469 / % possible obs: 91 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.037 |
Reflection shell | Resolution: 1.62→1.69 Å / Redundancy: 2.8 % / % possible all: 62.2 |
Reflection | *PLUS Highest resolution: 1.62 Å / Num. measured all: 78987 |
-Processing
Software |
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Refinement | Resolution: 1.62→7.5 Å / σ(F): 1.5 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B 13 GLU B 14 ALA B 15 (EXCEPT C AND O) GLU B 51 (CG, CD, OE1, OE2) ARG B 53 (NE, CZ, NH1, NH2) ASP B 67 GLY B 68 (N, ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B 13 GLU B 14 ALA B 15 (EXCEPT C AND O) GLU B 51 (CG, CD, OE1, OE2) ARG B 53 (NE, CZ, NH1, NH2) ASP B 67 GLY B 68 (N, CA) ARG B 84 (NE, CZ, NH1, NH2) ARG B 103 (NE, CZ, NH1, NH2) GLU B 116 (CG, CD, OE1, OE2) PRO B 135 ALA D 13 GLU D 14 ALA D 15 ASP D 36 (CG, OD1, OD2) ARG D 53 (NE, CZ, NH1, NH2) ASN D 82 (CG, OD1, ND2) ARG D 84 (NE, CZ, NH1, NH2) GLU D 101 (CG, CD, OE1, OE2) ARG D 103 (NE, CZ, NH1, NH2) GLU D 116 (CG, CD, OE1, OE2)
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Refinement step | Cycle: LAST / Resolution: 1.62→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.69 Å / % reflection obs: 62.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.189 |