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- PDB-8y24: X-ray crystal structure of ALiS4-Streptavidine complex with 10% g... -

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Basic information

Entry
Database: PDB / ID: 8y24
TitleX-ray crystal structure of ALiS4-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
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

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)51,81012
Polymers51,0594
Non-polymers7518
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-50 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.988, 85.622, 58.242
Angle α, β, γ (deg.)90.00, 98.97, 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-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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 609 / 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: 46.61 %
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: 80494 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.998 / Net I/σ(I): 9.3
Reflection shellResolution: 1.45→1.47 Å / Num. unique obs: 3997 / CC1/2: 0.686

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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→46.413 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1842 3931 4.89 %
Rwork0.1362 --
obs0.1385 80455 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→46.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 45 609 4210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053763
X-RAY DIFFRACTIONf_angle_d0.7945149
X-RAY DIFFRACTIONf_dihedral_angle_d14.3341218
X-RAY DIFFRACTIONf_chiral_restr0.081572
X-RAY DIFFRACTIONf_plane_restr0.004648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46760.26231530.19242761X-RAY DIFFRACTION100
1.4676-1.48620.24681330.17882720X-RAY DIFFRACTION100
1.4862-1.50580.19861330.16542714X-RAY DIFFRACTION100
1.5058-1.52640.20421280.15842725X-RAY DIFFRACTION100
1.5264-1.54820.23151410.14542715X-RAY DIFFRACTION100
1.5482-1.57130.2031440.13722773X-RAY DIFFRACTION100
1.5713-1.59590.19421150.13912687X-RAY DIFFRACTION100
1.5959-1.6220.23341210.13422785X-RAY DIFFRACTION100
1.622-1.650.18511510.13252688X-RAY DIFFRACTION100
1.65-1.680.18951280.12442774X-RAY DIFFRACTION100
1.68-1.71230.19421370.13012720X-RAY DIFFRACTION100
1.7123-1.74730.20441440.12982721X-RAY DIFFRACTION100
1.7473-1.78530.17941310.13022752X-RAY DIFFRACTION100
1.7853-1.82680.18321440.12912724X-RAY DIFFRACTION100
1.8268-1.87250.20171270.12642731X-RAY DIFFRACTION100
1.8725-1.92310.17981460.12632706X-RAY DIFFRACTION100
1.9231-1.97970.16751640.11892711X-RAY DIFFRACTION100
1.9797-2.04360.17621420.12552734X-RAY DIFFRACTION100
2.0436-2.11670.19291590.12942731X-RAY DIFFRACTION100
2.1167-2.20140.19771320.13142707X-RAY DIFFRACTION100
2.2014-2.30160.17071560.13672731X-RAY DIFFRACTION100
2.3016-2.42290.21411300.14042761X-RAY DIFFRACTION100
2.4229-2.57470.20241470.14462737X-RAY DIFFRACTION100
2.5747-2.77350.17661500.15072754X-RAY DIFFRACTION100
2.7735-3.05260.17121490.14372712X-RAY DIFFRACTION100
3.0526-3.49410.181440.12962755X-RAY DIFFRACTION100
3.4941-4.40170.16461290.12272770X-RAY DIFFRACTION100
4.4017-46.40.17481530.14782725X-RAY DIFFRACTION97

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