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

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Basic information

Entry
Database: PDB / ID: 1sri
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-DMB / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.65 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: Derived calculations / 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_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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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)26,0184
Polymers25,4772
Non-polymers5412
Water2,414134
1
A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0368
Polymers50,9554
Non-polymers1,0814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area11810 Å2
ΔGint-53 kcal/mol
Surface area18050 Å2
MethodPISA
2
A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,07216
Polymers101,9108
Non-polymers2,1628
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)95.600, 106.000, 47.900
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-DMB / 2-((3',5'-DIMETHYL-4'-HYDROXYPHENYL)AZO)BENZOIC ACID


Mass: 270.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.35 %
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: 1.65 Å / Num. obs: 28764 / Num. measured all: 156325 / Rmerge(I) obs: 0.064

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Processing

Software
NameClassification
PROFFTrefinement
PROLSQrefinement
RefinementResolution: 1.65→10 Å / σ(F): 1 /
RfactorNum. reflection
obs0.175 24078
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 40 134 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.024
X-RAY DIFFRACTIONp_angle_d0.0350.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0150.015
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_restr0.2890.289
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: 0.175
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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