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- PDB-1rsu: COMPLEX BETWEEN STREPTAVIDIN AND THE STREP-TAG II PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1rsu
TitleCOMPLEX BETWEEN STREPTAVIDIN AND THE STREP-TAG II PEPTIDE
Components
  • STREP-TAG II PEPTIDE
  • STREPTAVIDIN
KeywordsCOMPLEX (SIGNAL PROTEIN/PEPTIDE) / COMPLEX (SIGNAL PROTEIN-PEPTIDE) / SIGNAL PROTEIN / COMPLEX (SIGNAL PROTEIN-PEPTIDE) complex
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
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsKoepke, J. / Schmidt, T. / Skerra, A.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Molecular interaction between the Strep-tag affinity peptide and its cognate target, streptavidin.
Authors: Schmidt, T.G. / Koepke, J. / Frank, R. / Skerra, A.
#1: Journal: J.Chromatogr.,A / Year: 1994
Title: One-Step Affinity Purification of Bacterially Produced Proteins by Means of the 'Strep Tag' and Immobilized Recombinant Core Streptavidin
Authors: Schmidt, T.G. / Skerra, A.
#2: Journal: Protein Eng. / Year: 1993
Title: The Random Peptide Library-Assisted Engineering of a C-Terminal Affinity Peptide, Useful for the Detection and Purification of a Functional Ig Fv Fragment
Authors: Schmidt, T.G. / Skerra, A.
History
DepositionOct 19, 1995Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: STREPTAVIDIN
P: STREP-TAG II PEPTIDE


Theoretical massNumber of molelcules
Total (without water)14,6032
Polymers14,6032
Non-polymers00
Water1,892105
1
B: STREPTAVIDIN
P: STREP-TAG II PEPTIDE

B: STREPTAVIDIN
P: STREP-TAG II PEPTIDE

B: STREPTAVIDIN
P: STREP-TAG II PEPTIDE

B: STREPTAVIDIN
P: STREP-TAG II PEPTIDE


Theoretical massNumber of molelcules
Total (without water)58,4118
Polymers58,4118
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Unit cell
Length a, b, c (Å)58.400, 58.400, 176.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-201-

HOH

21B-202-

HOH

31B-203-

HOH

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Components

#1: Protein STREPTAVIDIN


Mass: 13341.454 Da / Num. of mol.: 1 / Fragment: RESIDUES 13 - 139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: PSA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Protein/peptide STREP-TAG II PEPTIDE


Mass: 1261.341 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.58 Å3/Da / Density % sol: 49 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
20.8 Mammonium sulfate1reservoir
3100 mMsodium phosphate1reservoir
1protein solution1drop0.002ml

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 13, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→37.38 Å / Num. obs: 16909 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0923

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISIICdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.7→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.213 --
Rwork0.18 --
obs0.18 16365 91.1 %
Displacement parametersBiso mean: 20.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 0 105 1150
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.589
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.75
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.163
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.755
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.163

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