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- PDB-8y2a: X-ray crystal structure of ALiS2-Streptavidine complex with 10% g... -

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Basic information

Entry
Database: PDB / ID: 8y2a
TitleX-ray crystal structure of ALiS2-Streptavidine complex with 10% glycerol using a high-pressure cryocooling method
ComponentsStreptavidin
KeywordsCYTOSOLIC PROTEIN / streptavidin
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
Chem-MT6 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsHigashiura, A. / Yamamoto, A. / Sugiyama, S.
CitationJournal: To Be Published
Title: Binding competition between substrates and cryoprotectants in protein crystals directly observed by a hybrid method of in-gel crystallization and high-pressure cryo-cooling in X-ray crystallography
Authors: Higashiura, A. / Sugiyama, S.
History
DepositionJan 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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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)52,1368
Polymers51,0594
Non-polymers1,0774
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-53 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.200, 85.842, 58.371
Angle α, β, γ (deg.)90.00, 99.17, 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 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#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.: 4 / Source method: obtained synthetically / Formula: C15H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.0, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.34→47.84 Å / Num. obs: 101487 / % possible obs: 98.8 % / Redundancy: 4.2 % / CC1/2: 0.999 / Net I/σ(I): 11.9
Reflection shellResolution: 1.34→1.36 Å / Num. unique obs: 4973 / CC1/2: 0.738

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→46.6 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1839 4978 4.92 %
Rwork0.1447 --
obs0.1467 101195 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.34→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3557 0 80 628 4265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043860
X-RAY DIFFRACTIONf_angle_d0.7935306
X-RAY DIFFRACTIONf_dihedral_angle_d12.7541300
X-RAY DIFFRACTIONf_chiral_restr0.081580
X-RAY DIFFRACTIONf_plane_restr0.005668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.360.3081440.21663198X-RAY DIFFRACTION97
1.36-1.370.23051550.18733136X-RAY DIFFRACTION98
1.37-1.390.22711710.17943166X-RAY DIFFRACTION97
1.39-1.410.21741620.17453121X-RAY DIFFRACTION97
1.41-1.420.21551720.17953141X-RAY DIFFRACTION96
1.42-1.440.22971540.17613178X-RAY DIFFRACTION98
1.44-1.460.21831640.17593191X-RAY DIFFRACTION97
1.46-1.490.19581590.17073163X-RAY DIFFRACTION98
1.49-1.510.19211610.15533191X-RAY DIFFRACTION98
1.51-1.530.21091810.15143175X-RAY DIFFRACTION98
1.53-1.560.1811700.13713190X-RAY DIFFRACTION99
1.56-1.590.1951670.12943151X-RAY DIFFRACTION98
1.59-1.620.16251490.12713250X-RAY DIFFRACTION98
1.62-1.650.16961700.12833191X-RAY DIFFRACTION99
1.65-1.690.20341740.12593212X-RAY DIFFRACTION98
1.69-1.730.1741810.13133192X-RAY DIFFRACTION99
1.73-1.770.19091840.13513194X-RAY DIFFRACTION99
1.77-1.820.18441640.13523249X-RAY DIFFRACTION99
1.82-1.870.191730.13583219X-RAY DIFFRACTION99
1.87-1.930.18931470.13343254X-RAY DIFFRACTION99
1.93-20.20171370.13653278X-RAY DIFFRACTION99
2-2.080.17421570.13893243X-RAY DIFFRACTION99
2.08-2.180.15981560.13583271X-RAY DIFFRACTION100
2.18-2.290.17791520.14033251X-RAY DIFFRACTION100
2.29-2.430.19781990.14963240X-RAY DIFFRACTION100
2.43-2.620.20441750.1543261X-RAY DIFFRACTION100
2.62-2.890.17351790.15273263X-RAY DIFFRACTION100
2.89-3.30.18211600.14393276X-RAY DIFFRACTION100
3.3-4.160.16021890.13123232X-RAY DIFFRACTION99
4.16-46.60.17681720.15313140X-RAY DIFFRACTION94

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