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- PDB-8xg6: X-ray crystal structure of Streptavidine without cryo-protectant ... -

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Basic information

Entry
Database: PDB / ID: 8xg6
TitleX-ray crystal structure of Streptavidine without cryo-protectant 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-PG6 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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)51,9808
Polymers51,0594
Non-polymers9214
Water12,935718
1
A: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0624
Polymers25,5302
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-15 kcal/mol
Surface area12470 Å2
MethodPISA
2
B: Streptavidin
C: 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 area3260 Å2
ΔGint-14 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.941, 85.948, 58.389
Angle α, β, γ (deg.)90.00, 99.21, 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-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / 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: 46.48 %
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: 1.31→47.87 Å / Num. obs: 109516 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.999 / Net I/σ(I): 13.1
Reflection shellResolution: 1.31→1.33 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5389 / CC1/2: 0.656

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→31.509 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1824 5410 4.95 %
Rwork0.1453 --
obs0.1471 109199 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→31.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 61 718 4361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043856
X-RAY DIFFRACTIONf_angle_d0.785282
X-RAY DIFFRACTIONf_dihedral_angle_d13.4911275
X-RAY DIFFRACTIONf_chiral_restr0.079587
X-RAY DIFFRACTIONf_plane_restr0.004666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.32490.28051790.223432X-RAY DIFFRACTION99
1.3249-1.34050.24881640.21163482X-RAY DIFFRACTION99
1.3405-1.35680.21971660.20143405X-RAY DIFFRACTION99
1.3568-1.3740.26421610.20443472X-RAY DIFFRACTION99
1.374-1.39210.23121780.19013448X-RAY DIFFRACTION99
1.3921-1.41110.25391900.18943409X-RAY DIFFRACTION99
1.4111-1.43130.24511820.17893405X-RAY DIFFRACTION99
1.4313-1.45260.25091920.17383431X-RAY DIFFRACTION100
1.4526-1.47530.2131920.16393436X-RAY DIFFRACTION99
1.4753-1.49950.1971740.14933479X-RAY DIFFRACTION100
1.4995-1.52540.18191730.14053464X-RAY DIFFRACTION100
1.5254-1.55310.20061690.14243466X-RAY DIFFRACTION100
1.5531-1.5830.20051810.14353428X-RAY DIFFRACTION100
1.583-1.61530.20991630.14223503X-RAY DIFFRACTION100
1.6153-1.65040.17991590.13983464X-RAY DIFFRACTION100
1.6504-1.68880.17391820.1323461X-RAY DIFFRACTION100
1.6888-1.73110.17991940.14193444X-RAY DIFFRACTION100
1.7311-1.77790.18481980.13853459X-RAY DIFFRACTION100
1.7779-1.83020.16652060.1363433X-RAY DIFFRACTION100
1.8302-1.88920.16251920.13633448X-RAY DIFFRACTION100
1.8892-1.95670.17961880.13213495X-RAY DIFFRACTION100
1.9567-2.03510.18551620.13583479X-RAY DIFFRACTION100
2.0351-2.12770.17411900.1393461X-RAY DIFFRACTION100
2.1277-2.23980.18311750.1363482X-RAY DIFFRACTION100
2.2398-2.38010.17221910.14293457X-RAY DIFFRACTION100
2.3801-2.56380.18251800.14733479X-RAY DIFFRACTION100
2.5638-2.82170.17951650.14513501X-RAY DIFFRACTION100
2.8217-3.22960.15612100.14843464X-RAY DIFFRACTION100
3.2296-4.06760.17181830.13423505X-RAY DIFFRACTION100
4.0676-31.50.1831710.14233497X-RAY DIFFRACTION98

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