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- PDB-8y29: X-ray crystal structure of ALiS2-Streptavidine complex without cr... -

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Basic information

Entry
Database: PDB / ID: 8y29
TitleX-ray crystal structure of ALiS2-Streptavidine complex without cryo-protectant using a high-pressure cryocooling method
ComponentsStreptavidin
KeywordsCYTOSOLIC PROTEIN / high-pressure cryo-cooling / 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-MT6 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsHigashiura, A. / Yamamoto, A. / Sugiyama, S.
Funding support1items
OrganizationGrant numberCountry
Other private
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)52,1368
Polymers51,0594
Non-polymers1,0774
Water11,512639
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-52 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.044, 85.983, 58.659
Angle α, β, γ (deg.)90.00, 99.16, 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-MT6 / methyl 3-(4-oxo-4,5-dihydrofuro[3,2-c]pyridin-2-yl)benzoate


Mass: 269.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
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: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.42→48.03 Å / Num. obs: 85824 / % possible obs: 99 % / Redundancy: 4.3 % / CC1/2: 0.999 / Net I/σ(I): 10.6
Reflection shellResolution: 1.42→1.45 Å / Num. unique obs: 4343 / CC1/2: 0.688

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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: 1.42→46.44 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1923 4317 5.03 %
Rwork0.1429 --
obs0.1454 85782 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 80 639 4229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053785
X-RAY DIFFRACTIONf_angle_d0.7995201
X-RAY DIFFRACTIONf_dihedral_angle_d11.5991270
X-RAY DIFFRACTIONf_chiral_restr0.083568
X-RAY DIFFRACTIONf_plane_restr0.004654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.31441370.22342667X-RAY DIFFRACTION98
1.44-1.450.23861320.20672695X-RAY DIFFRACTION98
1.45-1.470.25051480.18972713X-RAY DIFFRACTION98
1.47-1.490.22961500.18312624X-RAY DIFFRACTION99
1.49-1.510.22551350.16882749X-RAY DIFFRACTION98
1.51-1.530.25671340.16552681X-RAY DIFFRACTION99
1.53-1.550.22591670.15922673X-RAY DIFFRACTION98
1.55-1.570.22071530.14752694X-RAY DIFFRACTION99
1.57-1.60.22861750.14742629X-RAY DIFFRACTION99
1.6-1.630.20891390.14072734X-RAY DIFFRACTION99
1.63-1.650.19731500.13372686X-RAY DIFFRACTION99
1.65-1.680.1991300.13142755X-RAY DIFFRACTION99
1.68-1.720.20151310.13442676X-RAY DIFFRACTION99
1.72-1.750.19431310.14042748X-RAY DIFFRACTION99
1.75-1.790.20441430.14192701X-RAY DIFFRACTION99
1.79-1.830.18651310.13672737X-RAY DIFFRACTION99
1.83-1.880.1941390.13382732X-RAY DIFFRACTION99
1.88-1.930.16351370.13162706X-RAY DIFFRACTION99
1.93-1.980.18671460.12952719X-RAY DIFFRACTION99
1.98-2.050.21551320.13512770X-RAY DIFFRACTION99
2.05-2.120.18041530.1392708X-RAY DIFFRACTION100
2.12-2.210.17321410.13612745X-RAY DIFFRACTION100
2.21-2.310.2071510.14022725X-RAY DIFFRACTION100
2.31-2.430.19741480.14652734X-RAY DIFFRACTION100
2.43-2.580.19061290.1462780X-RAY DIFFRACTION100
2.58-2.780.18751500.15112761X-RAY DIFFRACTION100
2.78-3.060.17141490.14932740X-RAY DIFFRACTION100
3.06-3.50.19171580.13772749X-RAY DIFFRACTION100
3.5-4.410.17581560.12692743X-RAY DIFFRACTION99
4.41-46.440.18381420.14982691X-RAY DIFFRACTION95

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