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- PDB-8xg4: X-ray crystal structure of streptavidin flash-cooled in 30% glyce... -

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Basic information

Entry
Database: PDB / ID: 8xg4
TitleX-ray crystal structure of streptavidin flash-cooled in 30% glycerol 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 / Chem-PG6 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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)52,08612
Polymers51,0594
Non-polymers1,0278
Water11,530640
1
A: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9945
Polymers25,5302
Non-polymers4653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-16 kcal/mol
Surface area11170 Å2
MethodPISA
2
B: Streptavidin
C: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0927
Polymers25,5302
Non-polymers5635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-16 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.739, 85.686, 58.228
Angle α, β, γ (deg.)90.00, 99.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Streptavidin


Mass: 12764.833 Da / Num. of mol.: 4 / Fragment: UNP residues 39-159 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629

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Non-polymers , 5 types, 648 molecules

#2: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: 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
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.0, 20% PEG1,000

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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: 1.38→47.75 Å / Num. obs: 92788 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.4
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4543 / CC1/2: 0.757 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→46.164 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1693 4466 4.83 %
Rwork0.136 --
obs0.1376 92416 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→46.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 0 60 640 4279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043873
X-RAY DIFFRACTIONf_angle_d0.7675313
X-RAY DIFFRACTIONf_dihedral_angle_d15.3131287
X-RAY DIFFRACTIONf_chiral_restr0.08591
X-RAY DIFFRACTIONf_plane_restr0.004670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.39570.24641680.21152826X-RAY DIFFRACTION99
1.3957-1.41210.251520.20292901X-RAY DIFFRACTION99
1.4121-1.42930.28111570.19732896X-RAY DIFFRACTION99
1.4293-1.44740.2351510.18682895X-RAY DIFFRACTION99
1.4474-1.46650.22041320.17222936X-RAY DIFFRACTION99
1.4665-1.48660.21731510.1662915X-RAY DIFFRACTION99
1.4866-1.50780.2181500.1592928X-RAY DIFFRACTION99
1.5078-1.53030.18031270.15262920X-RAY DIFFRACTION100
1.5303-1.55420.21691310.14222923X-RAY DIFFRACTION100
1.5542-1.57970.20841660.13382894X-RAY DIFFRACTION99
1.5797-1.60690.18881400.12883001X-RAY DIFFRACTION100
1.6069-1.63620.16431460.12322886X-RAY DIFFRACTION100
1.6362-1.66760.17341510.11372961X-RAY DIFFRACTION100
1.6676-1.70170.15611320.11962919X-RAY DIFFRACTION100
1.7017-1.73870.21781440.12362944X-RAY DIFFRACTION100
1.7387-1.77910.18271430.12942940X-RAY DIFFRACTION100
1.7791-1.82360.17891530.12572932X-RAY DIFFRACTION100
1.8236-1.87290.1441620.12072932X-RAY DIFFRACTION100
1.8729-1.9280.16011680.12232923X-RAY DIFFRACTION100
1.928-1.99030.17821600.12772925X-RAY DIFFRACTION100
1.9903-2.06140.16831400.12912936X-RAY DIFFRACTION100
2.0614-2.14390.16951540.12542961X-RAY DIFFRACTION100
2.1439-2.24150.1521600.12482950X-RAY DIFFRACTION100
2.2415-2.35970.17351500.13262929X-RAY DIFFRACTION100
2.3597-2.50750.18281590.14282943X-RAY DIFFRACTION100
2.5075-2.70110.15711350.14082970X-RAY DIFFRACTION100
2.7011-2.97290.17191320.14162985X-RAY DIFFRACTION100
2.9729-3.4030.1571430.13222973X-RAY DIFFRACTION100
3.403-4.28690.14171630.12372962X-RAY DIFFRACTION100
4.2869-46.10.15621460.14722944X-RAY DIFFRACTION98

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