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- PDB-8zr2: Cocrystallization of engineered streptavidin with C9 oligo DNA -

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Basic information

Entry
Database: PDB / ID: 8zr2
TitleCocrystallization of engineered streptavidin with C9 oligo DNA
ComponentsStreptavidin
KeywordsUNKNOWN FUNCTION / Biotin-binding protein
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
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMinamihata, K. / Adachi, M.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Rsc Adv / Year: 2025
Title: Dual-functional co-crystal of streptavidin and ssDNA: electrostatic assembly with positively charged peptide tags.
Authors: Nagatani, A. / Minamihata, K. / Adachi, M. / Wakabayashi, R. / Goto, M. / Kamiya, N.
History
DepositionJun 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 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


Theoretical massNumber of molelcules
Total (without water)56,7504
Polymers56,7504
Non-polymers00
Water1,00956
1
A: Streptavidin
B: Streptavidin

A: Streptavidin
B: Streptavidin


Theoretical massNumber of molelcules
Total (without water)56,7504
Polymers56,7504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8790 Å2
ΔGint-48 kcal/mol
Surface area20400 Å2
MethodPISA
2
C: Streptavidin

C: Streptavidin

D: Streptavidin

D: Streptavidin


Theoretical massNumber of molelcules
Total (without water)56,7504
Polymers56,7504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
crystal symmetry operation3_555x+1/2,y+1/2,z1
crystal symmetry operation4_454-x-1/2,y+1/2,-z-11
Buried area8290 Å2
ΔGint-52 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.937, 80.986, 77.316
Angle α, β, γ (deg.)90.00, 91.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-201-

HOH

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Components

#1: Protein
Streptavidin


Mass: 14187.479 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22629
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 8 / Details: 20 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46.54 Å / Num. obs: 17327 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.165 / Net I/σ(I): 7.63
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1265 / CC1/2: 0.633 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNG

6lng


Resolution: 2.5→46.54 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3456 855 4.94 %
Rwork0.2344 --
obs0.2399 17315 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 0 56 3676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083712
X-RAY DIFFRACTIONf_angle_d1.1445084
X-RAY DIFFRACTIONf_dihedral_angle_d16.7441252
X-RAY DIFFRACTIONf_chiral_restr0.044568
X-RAY DIFFRACTIONf_plane_restr0.004640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65640.40071410.2672691X-RAY DIFFRACTION100
2.6564-2.86150.38731450.24732765X-RAY DIFFRACTION100
2.8615-3.14940.35871370.24132709X-RAY DIFFRACTION100
3.1494-3.6050.39451420.22112743X-RAY DIFFRACTION100
3.605-4.54130.3121550.21472749X-RAY DIFFRACTION100
4.5413-46.540.31191350.24732803X-RAY DIFFRACTION100

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