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- PDB-8y25: X-ray crystal structure of ALiS4-Streptavidine complex with 20% g... -

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Basic information

Entry
Database: PDB / ID: 8y25
TitleX-ray crystal structure of ALiS4-Streptavidine complex with 20% glycerol using a high-pressure cryocooling method
ComponentsStreptavidin
KeywordsCYTOSOLIC PROTEIN / high-pressure cryo-cooling / 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
DI(HYDROXYETHYL)ETHER / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHigashiura, A. / Yamamoto, A. / Sugiyama, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other private Japan
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,90213
Polymers51,0594
Non-polymers8439
Water10,701594
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-54 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.071, 85.008, 58.441
Angle α, β, γ (deg.)90.00, 99.04, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
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: Dec 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→47.75 Å / Num. obs: 78936 / % possible obs: 98.3 % / Redundancy: 4.3 % / CC1/2: 0.998 / Net I/σ(I): 9
Reflection shellResolution: 1.45→1.47 Å / Num. unique obs: 3871 / CC1/2: 0.748

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→46.486 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1881 3873 4.91 %
Rwork0.1391 --
obs0.1416 78891 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→46.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 48 594 4211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053800
X-RAY DIFFRACTIONf_angle_d0.7895201
X-RAY DIFFRACTIONf_dihedral_angle_d12.2551235
X-RAY DIFFRACTIONf_chiral_restr0.082577
X-RAY DIFFRACTIONf_plane_restr0.003655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46760.27411410.21512639X-RAY DIFFRACTION96
1.4676-1.48620.281290.21012632X-RAY DIFFRACTION97
1.4862-1.50580.28291330.20242620X-RAY DIFFRACTION96
1.5058-1.52640.24321360.17822651X-RAY DIFFRACTION97
1.5264-1.54820.21281480.16552635X-RAY DIFFRACTION97
1.5482-1.57130.20961420.15472671X-RAY DIFFRACTION98
1.5713-1.59590.22451370.15382596X-RAY DIFFRACTION97
1.5959-1.6220.22181420.15152702X-RAY DIFFRACTION97
1.622-1.650.21261390.142633X-RAY DIFFRACTION98
1.65-1.680.21571350.1292688X-RAY DIFFRACTION97
1.68-1.71230.21241510.1322645X-RAY DIFFRACTION98
1.7123-1.74730.20121190.13252671X-RAY DIFFRACTION98
1.7473-1.78530.24191320.1392654X-RAY DIFFRACTION98
1.7853-1.82680.1991310.13862699X-RAY DIFFRACTION98
1.8268-1.87250.17681280.13642711X-RAY DIFFRACTION99
1.8725-1.92310.20151340.12912666X-RAY DIFFRACTION98
1.9231-1.97970.18371470.1272689X-RAY DIFFRACTION99
1.9797-2.04360.19531060.12922695X-RAY DIFFRACTION99
2.0436-2.11660.21341150.13392729X-RAY DIFFRACTION99
2.1166-2.20140.20271360.12952687X-RAY DIFFRACTION99
2.2014-2.30160.18971340.13312730X-RAY DIFFRACTION99
2.3016-2.42290.18731700.13762665X-RAY DIFFRACTION99
2.4229-2.57470.19131350.1412737X-RAY DIFFRACTION99
2.5747-2.77350.19121420.14682726X-RAY DIFFRACTION99
2.7735-3.05250.18931540.14052701X-RAY DIFFRACTION100
3.0525-3.49410.17241520.12672715X-RAY DIFFRACTION100
3.4941-4.40170.13661550.12192725X-RAY DIFFRACTION99
4.4017-46.4860.18031500.15422706X-RAY DIFFRACTION97

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