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- PDB-8zr1: Cocrystallization of engineered streptavidin with A9 oligo DNA -

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Basic information

Entry
Database: PDB / ID: 8zr1
TitleCocrystallization of engineered streptavidin with A9 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: 2.601 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
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-50 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.084, 58.006, 57.791
Angle α, β, γ (deg.)90.65, 107.54, 98.84
Int Tables number1
Space group name H-MP1

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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.: 164 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 8 / Details: 10 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: 2.6→100 Å / Num. obs: 16710 / % possible obs: 97.5 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.14 / Net I/av σ(I): 8.8 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.690.51416700.5990.8660.5140.7272.38597.3
2.69-2.80.37416640.760.9290.3740.5292.11997.1
2.8-2.930.30416730.8570.9610.3040.432.36697.7
2.93-3.080.26416880.8510.9590.2640.3732.4297.7
3.08-3.280.21716480.8850.9690.2170.3072.50697.1
3.28-3.530.15216600.9510.9870.1520.2152.59397.4
3.53-3.880.10616950.9710.9930.1060.152.42697.9
3.88-4.450.09116820.9720.9930.0910.1292.64797.8
4.45-5.60.08416580.980.9950.0840.1192.6697.6
5.6-1000.08716720.9740.9930.0870.1232.67897.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNG

6lng


Resolution: 2.601→37.662 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2815 836 5.01 %
Rwork0.1975 --
obs0.2016 16697 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→37.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 0 164 3784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093712
X-RAY DIFFRACTIONf_angle_d1.165084
X-RAY DIFFRACTIONf_dihedral_angle_d16.4991252
X-RAY DIFFRACTIONf_chiral_restr0.046568
X-RAY DIFFRACTIONf_plane_restr0.005640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6011-2.76410.37061330.27812516X-RAY DIFFRACTION92
2.7641-2.97740.33661390.23862655X-RAY DIFFRACTION98
2.9774-3.27690.31661420.20232687X-RAY DIFFRACTION97
3.2769-3.75070.27861390.18112655X-RAY DIFFRACTION97
3.7507-4.7240.24331410.15622671X-RAY DIFFRACTION98
4.724-37.6620.24321420.20312677X-RAY DIFFRACTION98

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