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- PDB-4y5d: CRYSTAL STRUCTURE OF ALiS2-STREPTAVIDIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 4y5d
TitleCRYSTAL STRUCTURE OF ALiS2-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 ...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-MT6 / Chem-PE3 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsSugiyama, S. / Terai, T. / Kohno, M. / Ishida, H. / Nagano, T.
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

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)53,49311
Polymers51,4084
Non-polymers2,0857
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-47 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.927, 83.774, 45.947
Angle α, β, γ (deg.)90.00, 98.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Streptavidin


Mass: 12851.911 Da / Num. of mol.: 4 / Fragment: UNP residues 39-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Streptomyces avidinii (bacteria) / References: UniProt: P22629

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Non-polymers , 5 types, 420 molecules

#2: Chemical ChemComp-MT6 / methyl 3-(4-oxo-4,5-dihydrofuro[3,2-c]pyridin-2-yl)benzoate


Mass: 269.252 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H11NO4
#3: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M Mes-NaOH (pH6.0), 45%(w/v) PEG1000 / PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 132391 / % possible obs: 98.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.9
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.7 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.649 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17376 6643 5 %RANDOM
Rwork0.1377 ---
obs0.13951 125634 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.943 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.03 Å2
2--0.57 Å20 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3640 0 106 413 4159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.024061
X-RAY DIFFRACTIONr_bond_other_d0.0020.023571
X-RAY DIFFRACTIONr_angle_refined_deg2.2891.9255589
X-RAY DIFFRACTIONr_angle_other_deg1.06938189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1395535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76323.797158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79815537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2771517
X-RAY DIFFRACTIONr_chiral_restr0.1570.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024851
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021012
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_it3.5341.462077
X-RAY DIFFRACTIONr_mcbond_other3.5111.462076
X-RAY DIFFRACTIONr_mcangle_it3.9312.1882633
X-RAY DIFFRACTIONr_mcangle_other3.9332.1882634
X-RAY DIFFRACTIONr_scbond_it4.2541.7331984
X-RAY DIFFRACTIONr_scbond_other4.2531.7341985
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7462.492957
X-RAY DIFFRACTIONr_long_range_B_refined4.75113.5864884
X-RAY DIFFRACTIONr_long_range_B_other4.63313.0334664
X-RAY DIFFRACTIONr_rigid_bond_restr5.70637632
X-RAY DIFFRACTIONr_sphericity_free25.1045116
X-RAY DIFFRACTIONr_sphericity_bonded11.31257837
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 461 -
Rwork0.256 9018 -
obs--95.02 %

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