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- PDB-8xg5: X-ray crystal structure of streptavidin flash-cooled in 30% PEG10... -

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Basic information

Entry
Database: PDB / ID: 8xg5
TitleX-ray crystal structure of streptavidin flash-cooled in 30% PEG1000 at ambient pressure
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: 1.4 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
DepositionDec 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: 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)51,8549
Polymers51,0594
Non-polymers7955
Water8,449469
1
A: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9184
Polymers25,5302
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-16 kcal/mol
Surface area11650 Å2
MethodPISA
2
B: Streptavidin
C: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9365
Polymers25,5302
Non-polymers4063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-16 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.752, 84.946, 58.345
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 / Fragment: Avidin-like / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 1.4→47.69 Å / Num. obs: 88033 / % possible obs: 99.5 % / Redundancy: 4.2 % / CC1/2: 0.999 / Net I/σ(I): 13.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4382 / CC1/2: 0.712

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→33.574 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1826 4435 5.05 %
Rwork0.1462 --
obs0.148 87908 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→33.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 50 469 4034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053794
X-RAY DIFFRACTIONf_angle_d0.7915201
X-RAY DIFFRACTIONf_dihedral_angle_d11.6881243
X-RAY DIFFRACTIONf_chiral_restr0.083581
X-RAY DIFFRACTIONf_plane_restr0.004655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.28971470.22362809X-RAY DIFFRACTION99
1.4159-1.43260.28491480.21642762X-RAY DIFFRACTION100
1.4326-1.450.2621430.2142777X-RAY DIFFRACTION100
1.45-1.46840.25941480.1952785X-RAY DIFFRACTION100
1.4684-1.48770.22911450.17952776X-RAY DIFFRACTION100
1.4877-1.50810.19981390.17152812X-RAY DIFFRACTION100
1.5081-1.52960.25411670.16462730X-RAY DIFFRACTION100
1.5296-1.55250.21421590.15632781X-RAY DIFFRACTION100
1.5525-1.57670.19011790.14762770X-RAY DIFFRACTION100
1.5767-1.60260.19841590.14612783X-RAY DIFFRACTION100
1.6026-1.63020.2021580.13652755X-RAY DIFFRACTION100
1.6302-1.65980.19441230.13062823X-RAY DIFFRACTION100
1.6598-1.69180.20351370.13172780X-RAY DIFFRACTION100
1.6918-1.72630.21081360.13622848X-RAY DIFFRACTION100
1.7263-1.76380.18171480.13522776X-RAY DIFFRACTION100
1.7638-1.80490.17561300.13592799X-RAY DIFFRACTION100
1.8049-1.850.18231400.12392796X-RAY DIFFRACTION100
1.85-1.90.15861370.12632801X-RAY DIFFRACTION100
1.9-1.95590.16211540.12572809X-RAY DIFFRACTION100
1.9559-2.0190.15511390.13092818X-RAY DIFFRACTION100
2.019-2.09120.15741560.13342765X-RAY DIFFRACTION100
2.0912-2.17490.17691520.13122795X-RAY DIFFRACTION100
2.1749-2.27390.16231350.14112800X-RAY DIFFRACTION100
2.2739-2.39370.19691520.14652795X-RAY DIFFRACTION100
2.3937-2.54360.17621440.15252840X-RAY DIFFRACTION100
2.5436-2.73990.17711480.14822797X-RAY DIFFRACTION100
2.7399-3.01550.16571580.15462799X-RAY DIFFRACTION100
3.0155-3.45150.18911550.14152806X-RAY DIFFRACTION100
3.4515-4.3470.17011610.13712723X-RAY DIFFRACTION97
4.347-33.50.1791380.16522563X-RAY DIFFRACTION89

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