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- PDB-1stp: STRUCTURAL ORIGINS OF HIGH-AFFINITY BIOTIN BINDING TO STREPTAVIDIN -

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Basic information

Entry
Database: PDB / ID: 1stp
TitleSTRUCTURAL ORIGINS OF HIGH-AFFINITY BIOTIN BINDING TO STREPTAVIDIN
ComponentsSTREPTAVIDIN COMPLEX WITH BIOTIN
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
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsWeber, P.C. / Salemme, F.R.
Citation
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.
#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.
History
DepositionMar 12, 1992Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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_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_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 COMPLEX WITH BIOTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7492
Polymers16,5051
Non-polymers2441
Water1,51384
1
A: STREPTAVIDIN COMPLEX WITH BIOTIN
hetero molecules

A: STREPTAVIDIN COMPLEX WITH BIOTIN
hetero molecules

A: STREPTAVIDIN COMPLEX WITH BIOTIN
hetero molecules

A: STREPTAVIDIN COMPLEX WITH BIOTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9978
Polymers66,0194
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area11350 Å2
ΔGint-42 kcal/mol
Surface area18340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.400, 99.400, 125.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein STREPTAVIDIN COMPLEX WITH BIOTIN


Mass: 16504.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 4.71 Å3/Da / Density % sol: 73.86 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 8 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19-13 %(w/v)PEG80001reservoir
31 M1reservoircan be substituted with 2 M NaCl or KClLiCl
2citric acid-sodium phsophate1reservoirin pH6.0-8.0

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Data collection

Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 13496 / Num. measured all: 89393 / Rmerge(I) obs: 0.052

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.22 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 16 84 1001
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / Num. reflection obs: 7379 / Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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