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- PDB-1srf: STRUCTURE-BASED DESIGN OF SYNTHETIC AZOBENZENE LIGANDS FOR STREPT... -

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Basic information

Entry
Database: PDB / ID: 1srf
TitleSTRUCTURE-BASED DESIGN OF SYNTHETIC AZOBENZENE LIGANDS FOR STREPTAVIDIN
ComponentsSTREPTAVIDIN
KeywordsBIOTIN-BINDING PROTEIN
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin ...Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-MTB / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWeber, P.C. / Salemme, F.R.
Citation
Journal: J.Am.Chem.Soc. / Year: 1994
Title: Structure-Based Design of Synthetic Azobenzene Ligands for Streptavidin
Authors: Weber, P.C. / Pantoliano, M.W. / Simons, D.M. / Salemme, F.R.
#1: Journal: J.Am.Chem.Soc. / Year: 1992
Title: Crystallographic and Thermodynamic Comparison of Natural and Synthetic Ligands Bound to Streptavidin
Authors: Weber, P.C. / Wendoloski, J.J. / Pantoliano, M.W. / Salemme, F.R.
#2: Journal: Science / Year: 1989
Title: Structural Origins of High-Affinity Biotin Binding to Streptavidin
Authors: Weber, P.C. / Ohlendorf, D.H. / Wendoloski, J.J. / Salemme, F.R.
History
DepositionFeb 17, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 10, 2012Group: Other
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0744
Polymers25,4772
Non-polymers5972
Water2,864159
1
A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1488
Polymers50,9554
Non-polymers1,1934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)94.200, 104.800, 47.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein STREPTAVIDIN


Mass: 12738.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical ChemComp-MTB / 2-((3'-TERTBUTYL-4'-HYDROXYPHENYL)AZO)BENZOIC ACID


Mass: 298.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal grow
*PLUS
Temperature: 30 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135-40 %satammonium sulfate1drop
240 %(v/v)MPD1drop
350 %MPD1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 14692 / Num. measured all: 57038 / Rmerge(I) obs: 0.071

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Processing

Software
NameClassification
PROFFTrefinement
PROLSQrefinement
RefinementResolution: 2→10 Å / σ(F): 1 /
RfactorNum. reflection
obs0.18 12231
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 44 159 1939
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.013
X-RAY DIFFRACTIONp_angle_d0.0250.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0080.008
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1740.174
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ/PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_chiral_restr

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