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- PDB-1kl5: an engineered streptavidin with improved affinity for the strep-t... -

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Basic information

Entry
Database: PDB / ID: 1kl5
Titlean engineered streptavidin with improved affinity for the strep-tag II peptide : SAm2-StrepII
Components
  • strep-tag II
  • 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: 1.8 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
F: strep-tag II
G: strep-tag II
H: strep-tag II


Theoretical massNumber of molelcules
Total (without water)58,1118
Polymers58,1118
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12480 Å2
ΔGint-78 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.394, 86.581, 47.235
Angle α, β, γ (deg.)90.00, 99.10, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is one of the teramers in the asymmetric unit

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Components

#1: Protein
streptavidin


Mass: 13353.535 Da / Num. of mol.: 4 / Mutation: E44I,S45G,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


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.: 167 / 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: 7.5
Details: 100 mM Na2HPO4, 1.2-M (NH4)2SO4, pH 7.50, 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: Sep 25, 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: 1.8→48 Å / Num. obs: 41071 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rsym value: 0.04 / Net I/σ(I): 19.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.81 % / Mean I/σ(I) obs: 3 / Num. unique all: 3998 / Rsym value: 0.352 / % possible all: 93.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 99 Å / Num. measured all: 120275 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 93.2 %

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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: 1.8→48 Å / SU B: 3.86 / SU ML: 0.122 / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 2013 4.9 %RANDOM
Rwork0.1779 ---
obs0.1801 38659 94.56 %-
Displacement parametersBiso mean: 23.282 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å20.14 Å2
2--0.25 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 0 167 3957
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.021
X-RAY DIFFRACTIONp_angle_d2.6791.885
LS refinement shellResolution: 1.8→1.85 Å
RfactorNum. reflection% reflection
Rfree0.35 142 -
Rwork0.28 --
obs-2788 92.87 %
Refinement
*PLUS
Rfactor obs: 0.178 / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.6791.885
LS refinement shell
*PLUS
Rfactor Rfree: 0.35 / Rfactor Rwork: 0.28

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