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Open data
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Basic information
Entry | Database: PDB / ID: 2rtp | |||||||||
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Title | STREPTAVIDIN-2-IMINOBIOTIN COMPLEX, PH 3.25, SPACE GROUP I222 | |||||||||
![]() | STREPTAVIDIN | |||||||||
![]() | BIOTIN-BINDING PROTEIN / STREPTAVIDIN-2-IMINOBIOTIN / PH 3.25 | |||||||||
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 | ![]() | 114.7 KB | Display | ![]() |
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PDB format | ![]() | 92.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.6 KB | Display | ![]() |
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Full document | ![]() | 462.3 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 21.1 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 ![]() 2rtdC ![]() 2rteC ![]() 2rtfC ![]() 2rtgC ![]() 2rthC ![]() 2rtiC ![]() 2rtjC ![]() 2rtkC ![]() 2rtlC ![]() 2rtmC ![]() 2rtnC ![]() 2rtoC ![]() 2rtqC ![]() 2rtrC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999816, -0.018746, -0.004086), 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: 2.1 Å3/Da / Density % sol: 21.8 % 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: 3.25 Details: ROOM TEMPERATURE, PH 3.25. SYNTHETIC MOTHER LIQUOR OF 50% SATURATED AMMONIUM SULFATE, 50% 1 M POTASSIUM ACETATE, 170 MM 2-IMINOBIOTIN, PH ADJUSTED TO 3.25 | ||||||||||||||||||||||||||||||
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 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: 46023 / % possible obs: 65 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 1.5→1.57 Å / Redundancy: 2.6 % / % possible all: 27.3 |
Reflection | *PLUS Highest resolution: 1.26 Å / Num. measured all: 121470 |
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Processing
Software |
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Refinement | Resolution: 1.5→7.5 Å / σ(F): 2.2 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, HG1, HG2, CD, OE1, OE2) ARG B 53 (NE, HE, CZ, NH1, HH11, HH12, ...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, 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 99 ALA B 100 GLU B 101 (CG, HG1, HG2, CD, OE1, OE2) ARG B 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU B 116 (CG, HG1, HG2, CD, OE1, OE2) PRO B 135 ALA D 13 GLU D 14 ALA D 15 (EXCEPT C AND O) 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 (SIDE CHAIN) 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, OE2) RESIDUES B 60-B 69 AND D 60-D 69 WERE REFINED IN TWO 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 B 22 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. HOH 525, HOH 1464, HOH 1491, HOH 1516 WERE USED TO ACCOUNT FOR DENSITY DUE TO THIS CONFORMER OF TYR B 22. 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: 27.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.206 |