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Open data
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Basic information
Entry | Database: PDB / ID: 2rtd | ||||||
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Title | STREPTAVIDIN-BIOTIN COMPLEX, PH 1.39, SPACE GROUP I222 | ||||||
![]() | STREPTAVIDIN | ||||||
![]() | BIOTIN-BINDING PROTEIN / STREPTAVIDIN-BIOTIN / PH 1.39 | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Katz, B.A. | ||||||
![]() | ![]() Title: Binding of biotin to streptavidin stabilizes intersubunit salt bridges between Asp61 and His87 at low pH. Authors: Katz, B.A. #1: ![]() 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: ![]() 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: ![]() Title: Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design Authors: Katz, B.A. #4: ![]() Title: Topochemical Catalysis Achieved by Structure-Based Ligand Design Authors: Katz, B.A. / Cass, R.T. / Liu, B. / Arze, R. / Collins, N. #5: ![]() Title: Topochemistry for Preparing Ligands that Dimerize Receptors Authors: Katz, B.A. / Stroud, R.M. / Collins, N. / Liu, B. / Arze, R. #6: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.8 KB | Display | ![]() |
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PDB format | ![]() | 91.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.6 KB | Display | ![]() |
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Full document | ![]() | 456.4 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2izaC ![]() 2izbC ![]() 2izcC ![]() 2izdC ![]() 2izeC ![]() 2izfC ![]() 2izgC ![]() 2izhC ![]() 2iziC ![]() 2izjC ![]() 2izkC ![]() 2izlC ![]() 2rtaC ![]() 2rtbC ![]() 2rtcC ![]() 2rteC ![]() 2rtfC ![]() 2rtgC ![]() 2rthC ![]() 2rtiC ![]() 2rtjC ![]() 2rtkC ![]() 2rtlC ![]() 2rtmC ![]() 2rtnC ![]() 2rtoC ![]() 2rtpC ![]() 2rtqC ![]() 2rtrC C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999253, -0.01986, -0.033155), Vector: |
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Components
#1: Protein | Mass: 14181.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 25.4 % 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: 1.39 Details: SYNTHETIC MOTHER LIQUOR OF 75% SATURATED AMMONIUM SULFATE, SODIUM FORMATE ADJUSTED TO PH 1.39. | ||||||||||||||||||||||||||||||
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 / 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: 45327 / Redundancy: 3.8 % / Rmerge(I) obs: 0.083 |
Reflection | *PLUS Highest resolution: 1.26 Å / Num. measured all: 173634 |
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Processing
Software |
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Refinement | Resolution: 1.65→7.5 Å / σ(F): 2.5 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B 13 GLU B 14 ALA B 15 TYR B 22 (SIDE CHAIN) GLU B 51 (CG, HG1, HG2, CD, OE1, OE2) ARG B 53 (NE, HE, CZ, NH1, HH11, ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B 13 GLU B 14 ALA B 15 TYR B 22 (SIDE CHAIN) 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) GLU B 101 (CG, HG1, HG2, CD, OE1, OE2 OF GLU B101) ARG B 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU B 116 (CG, HG1, HG2, CD, OE1, OE2) LYS B 134 (CB, HB1, HB2, CG, HG1, HG2) LYS B 134 (CD, HD1, HD2, NZ, HZ1, HZ2, HZ3) 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) TYR D 83 (CG AND OUTWARD) ARG D 84 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU D 101 (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, OE) RESIDUES B60-B69 AND D60-D69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP 61 AT LOW PH, ASP B 61 AND ASP D 61 UNDERGO LARGE SHIFTS IN CONFORMATION AND CHANGES IN HYDROGEN BONDING. THE LOOPS COMPRISING RESIDUES B 61-B 69 AND D 61-D 69 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 B22. PROPER REFINEMENT WITH XPLOR IS NOT POSSIBLE BECAUSE OF THE OVERLAP OF ONE CONFORMER WITH THE SYMMETRY RELATED COUNTERPART.
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Refinement step | Cycle: LAST / Resolution: 1.65→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.72 Å / % reflection obs: 50.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.21 / 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 |