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- PDB-5b5f: Crystal structure of ALiS3-Streptavidin complex -

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Basic information

Entry
Database: PDB / ID: 5b5f
TitleCrystal structure of ALiS3-Streptavidin complex
ComponentsStreptavidin
KeywordsBIOTIN-BINDING PROTEIN / high-strength agarose hydrogel
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-6F3 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSugiyama, S. / Terai, T. / Kakinouchi, K. / Fujikake, R. / Nagano, T. / Urano, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS KAKENHI25286051 Japan
JSPS KAKENHI25650051 Japan
JSPS KAKENHI23860028 Japan
CitationJournal: Chembiochem / Year: 2017
Title: Improving the Solubility of Artificial Ligands of Streptavidin to Enable More Practical Reversible Switching of Protein Localization in Cells
Authors: Tachibana, R. / Terai, T. / Boncompain, G. / Sugiyama, S. / Saito, N. / Perez, F. / Urano, Y.
History
DepositionMay 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9928
Polymers50,7754
Non-polymers1,2174
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-53 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.985, 84.621, 46.336
Angle α, β, γ (deg.)90.00, 99.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Streptavidin


Mass: 12693.756 Da / Num. of mol.: 4 / Fragment: UNP residues 40-159 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical
ChemComp-6F3 / N-methyl-3-(4-oxo-4,5-dihydrofuro[3,2-c]pyridin-2-yl)benzenesulfonamide


Mass: 304.321 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12N2O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES-NaOH (pH6.0), 35%(w/v) PEG 1000, 2.0% agarose hydrogel

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→57.27 Å / Num. obs: 134521 / % possible obs: 98 % / Redundancy: 4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.2
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.8 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y59

4y59


Resolution: 1.2→57.27 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.965 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 6773 5 %RANDOM
Rwork0.153 ---
obs0.155 127730 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20.02 Å2
2--0.34 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.2→57.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 84 401 4081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.023979
X-RAY DIFFRACTIONr_bond_other_d0.0020.023472
X-RAY DIFFRACTIONr_angle_refined_deg2.0611.9245491
X-RAY DIFFRACTIONr_angle_other_deg1.84437944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4525518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.60723.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78915532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7811518
X-RAY DIFFRACTIONr_chiral_restr0.1380.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024751
X-RAY DIFFRACTIONr_gen_planes_other0.010.021011
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5621.7642024
X-RAY DIFFRACTIONr_mcbond_other3.5581.7622023
X-RAY DIFFRACTIONr_mcangle_it4.0742.6452558
X-RAY DIFFRACTIONr_mcangle_other4.0732.6462559
X-RAY DIFFRACTIONr_scbond_it5.0392.0871955
X-RAY DIFFRACTIONr_scbond_other5.0372.0871956
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8173.0422934
X-RAY DIFFRACTIONr_long_range_B_refined5.18416.3524843
X-RAY DIFFRACTIONr_long_range_B_other5.04215.8494634
X-RAY DIFFRACTIONr_rigid_bond_restr7.85737451
X-RAY DIFFRACTIONr_sphericity_free25.1875131
X-RAY DIFFRACTIONr_sphericity_bonded11.80657608
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 423 -
Rwork0.33 9032 -
obs--93.21 %

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