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- PDB-8y23: X-ray crystal structure of ALiS4-Streptavidine complex without cr... -

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Basic information

Entry
Database: PDB / ID: 8y23
TitleX-ray crystal structure of ALiS4-Streptavidine complex 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-6FX / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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)52,1408
Polymers51,0594
Non-polymers1,0814
Water12,142674
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.918, 86.004, 58.402
Angle α, β, γ (deg.)90.00, 99.17, 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-6FX / methyl 5-(4-oxidanylidene-5~{H}-furo[3,2-c]pyridin-2-yl)pyridine-3-carboxylate / methyl 5-(4-oxo-4,5-dihydrofuro[3,2-c]pyridin-2-yl)nicotinate


Mass: 270.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H10N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.31 Å3/Da / Density % sol: 46.8 %
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: 1.48→47.89 Å / Num. obs: 76085 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.997 / Net I/σ(I): 9
Reflection shellResolution: 1.48→1.51 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3763 / CC1/2: 0.715

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→46.32 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1929 3805 5 %
Rwork0.1383 --
obs0.141 76050 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 80 674 4314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053795
X-RAY DIFFRACTIONf_angle_d0.7825207
X-RAY DIFFRACTIONf_dihedral_angle_d11.2791274
X-RAY DIFFRACTIONf_chiral_restr0.081566
X-RAY DIFFRACTIONf_plane_restr0.004655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.26661470.21622661X-RAY DIFFRACTION100
1.5-1.520.22691160.1942672X-RAY DIFFRACTION100
1.52-1.540.26921500.1912664X-RAY DIFFRACTION100
1.54-1.560.2631460.17532684X-RAY DIFFRACTION100
1.56-1.580.25311460.17822634X-RAY DIFFRACTION100
1.58-1.610.21971480.16112694X-RAY DIFFRACTION100
1.61-1.640.24491360.15262652X-RAY DIFFRACTION100
1.64-1.660.19491590.14292655X-RAY DIFFRACTION100
1.66-1.690.23221430.13612666X-RAY DIFFRACTION100
1.69-1.730.20721420.13572681X-RAY DIFFRACTION100
1.73-1.760.16841440.12622664X-RAY DIFFRACTION100
1.76-1.80.20491490.13022650X-RAY DIFFRACTION100
1.8-1.840.20121180.12642701X-RAY DIFFRACTION100
1.84-1.890.19621470.13182684X-RAY DIFFRACTION100
1.89-1.940.21151570.13242629X-RAY DIFFRACTION100
1.94-20.18671430.12832686X-RAY DIFFRACTION100
2-2.060.19081460.12712652X-RAY DIFFRACTION100
2.06-2.130.18381440.13022692X-RAY DIFFRACTION100
2.13-2.220.18121330.13062708X-RAY DIFFRACTION100
2.22-2.320.20851290.13252681X-RAY DIFFRACTION100
2.32-2.440.20231670.14322648X-RAY DIFFRACTION100
2.44-2.60.18861410.1422675X-RAY DIFFRACTION100
2.6-2.80.21181360.13882693X-RAY DIFFRACTION100
2.8-3.080.17541130.13982723X-RAY DIFFRACTION100
3.08-3.520.14881220.12932696X-RAY DIFFRACTION100
3.52-4.440.17191240.1242732X-RAY DIFFRACTION100
4.44-46.320.19261590.14932668X-RAY DIFFRACTION98

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