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- PDB-4y59: Crystal structure of ALiS1-Streptavidin complex -

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Basic information

Entry
Database: PDB / ID: 4y59
TitleCrystal structure of ALiS1-Streptavidin complex
ComponentsStreptavidin
KeywordsBIOTIN-Binding protein / Inhibitor
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-T21 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.22 Å
AuthorsSugiyama, S. / Terai, T. / Kohno, M. / Ishida, H. / Nagano, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS KAKENHI (Japan)25286051 Japan
JSPS KAKENHI (Japan)25650051 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Artificial Ligands of Streptavidin (ALiS): Discovery, Characterization, and Application for Reversible Control of Intracellular Protein Transport
Authors: Terai, T. / Kohno, M. / Boncompain, G. / Sugiyama, S. / Saito, N. / Fujikake, R. / Ueno, T. / Komatsu, T. / Hanaoka, K. / Okabe, T. / Urano, Y. / Perez, F. / Nagano, T.
History
DepositionFeb 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
C: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1768
Polymers51,0594
Non-polymers1,1174
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-54 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.843, 84.353, 46.156
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Streptavidin /


Mass: 12764.833 Da / Num. of mol.: 4 / Fragment: UNP residues 39-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical
ChemComp-T21 / 2-[3-(trifluoromethyl)phenyl]furo[3,2-c]pyridin-4(5H)-one


Mass: 279.214 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H8F3NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Hepes-NaOH (pH7.0), 50%(v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. obs: 129491 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.3
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.22→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.162 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15545 6519 5 %RANDOM
Rwork0.12458 ---
obs0.12615 122948 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.704 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20.01 Å2
2--0.73 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.22→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 80 411 4107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.024125
X-RAY DIFFRACTIONr_bond_other_d0.0020.023582
X-RAY DIFFRACTIONr_angle_refined_deg2.3431.9255720
X-RAY DIFFRACTIONr_angle_other_deg1.08338223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8175554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68223.75160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7615553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7111517
X-RAY DIFFRACTIONr_chiral_restr0.140.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025006
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021047
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_it2.6081.3622120
X-RAY DIFFRACTIONr_mcbond_other2.6081.3622119
X-RAY DIFFRACTIONr_mcangle_it2.8452.0422706
X-RAY DIFFRACTIONr_mcangle_other2.8452.0422707
X-RAY DIFFRACTIONr_scbond_it3.2361.5892005
X-RAY DIFFRACTIONr_scbond_other3.2351.5892006
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7812.2973015
X-RAY DIFFRACTIONr_long_range_B_refined3.85512.6784986
X-RAY DIFFRACTIONr_long_range_B_other3.74912.1794765
X-RAY DIFFRACTIONr_rigid_bond_restr6.10537707
X-RAY DIFFRACTIONr_sphericity_free24.2615130
X-RAY DIFFRACTIONr_sphericity_bonded9.12157869
LS refinement shellResolution: 1.22→1.251 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 476 -
Rwork0.162 8843 -
obs--97.4 %

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