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- PDB-1kl3: an engineered streptavidin with improved affinity for the strep-t... -

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Basic information

Entry
Database: PDB / ID: 1kl3
Titlean engineered streptavidin with improved affinity for the strep-tag II peptide : SAm1-StrepII
Components
  • strep-tag II peptide
  • streptavidin
KeywordsPEPTIDE BINDING PROTEIN / BIOTIN / PROTEIN ENGINEERING / STREP-TAG / STREPTAVIDIN
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 / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsKorndoerfer, I.P. / Skerra, A.
CitationJournal: Protein Sci. / Year: 2002
Title: Improved affinity of engineered streptavidin for the Strep-tag II peptide is due to a fixed open conformation of the lid-like loop at the binding site.
Authors: Korndorfer, I.P. / Skerra, A.
History
DepositionDec 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: streptavidin
B: streptavidin
C: streptavidin
D: streptavidin
E: strep-tag II peptide
F: strep-tag II peptide
G: strep-tag II peptide
H: strep-tag II peptide


Theoretical massNumber of molelcules
Total (without water)58,2318
Polymers58,2318
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12500 Å2
ΔGint-76 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.699, 86.339, 47.448
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is one of the tetramers in the asymmetric unit

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Components

#1: Protein
streptavidin


Mass: 13383.561 Da / Num. of mol.: 4 / Mutation: E44V,S45T,V47R
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: 1174.263 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: The strep-tag II peptide is chemically synthesized and was selected by synthetic peptide spot assays from a subset of strep-tag derivatives.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 100 mM Na2HPO4, 1.3-M (NH4)2SO4, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122 mg/mlprotein1drop
25 mMTris-HCl1droppH8.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 21, 2001 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→36 Å / Num. obs: 49002 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rsym value: 0.04 / Net I/σ(I): 23.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.38 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4648 / Rsym value: 0.348 / % possible all: 90.3
Reflection
*PLUS
Lowest resolution: 99 Å / Num. measured all: 126949 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 90.3 %

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Processing

Software
NameClassification
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1SWU

1swu


Resolution: 1.7→36 Å / SU B: 3.021 / SU ML: 0.101 / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 2430 5 %RANDOM
Rwork0.1746 ---
obs0.1768 46287 94.84 %-
Displacement parametersBiso mean: 25.447 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20.16 Å2
2--0.16 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 0 238 4054
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.021
X-RAY DIFFRACTIONp_angle_d2.7731.884
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_restr
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
LS refinement shellResolution: 1.7→1.75 Å
RfactorNum. reflection% reflection
Rfree0.43 156 -
Rwork0.41 --
obs-3228 90.34 %
Refinement
*PLUS
Rfactor obs: 0.175 / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.7731.884
LS refinement shell
*PLUS
Rfactor Rfree: 0.43 / Rfactor Rwork: 0.41

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