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- PDB-9i4r: N-terminal Oic streptag II in Sav E44V-S45T-V47R-D67A-K121R variant -

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Basic information

Entry
Database: PDB / ID: 9i4r
TitleN-terminal Oic streptag II in Sav E44V-S45T-V47R-D67A-K121R variant
Components
  • Oic-P-streptagII
  • Streptavidin
KeywordsPROTEIN BINDING / Artificial enzyme / peptide binding protein / streptag / 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
Biological speciesStreptomyces avidinii (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsWang, W. / Lau, K. / Pojer, F. / Larabi, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Synth / Year: 2025
Title: Biotin/Steptag dual cofactor system for assymetric abiotic transformation in artificial metalloenzymes
Authors: Wang, W. / Ji, X. / Acin, P.G. / Lau, K. / Pojer, F. / Ward, T.R. / Hu, X.
History
DepositionJan 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 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
B: Streptavidin
C: Streptavidin
D: Streptavidin
E: Streptavidin
F: Oic-P-streptagII
G: Oic-P-streptagII
H: Oic-P-streptagII
I: Oic-P-streptagII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1789
Polymers71,0868
Non-polymers921
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13080 Å2
ΔGint-72 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.550, 105.892, 51.246
Angle α, β, γ (deg.)90.000, 106.448, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Streptavidin


Mass: 16462.895 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: Protein/peptide
Oic-P-streptagII


Mass: 1308.481 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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

Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium citrate dibasic, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.84→19.48 Å / Num. obs: 39883 / % possible obs: 95.4 % / Redundancy: 2.7 % / Biso Wilson estimate: 19.93 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.134 / Net I/σ(I): 6
Reflection shellResolution: 1.844→1.876 Å / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1771 / CC1/2: 0.689 / Rrim(I) all: 1.044

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Processing

Software
NameVersionClassification
PHENIXdev_5373refinement
XDSJun 30, 2024 (BUILT 20240723)data reduction
Aimlessversion 0.8.1data scaling
PHENIXphasing
autoPROC1.0.5data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→19.48 Å / SU ML: 0.1734 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.7246
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2129 2039 5.14 %
Rwork0.1759 37633 -
obs0.1778 39672 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.38 Å2
Refinement stepCycle: LAST / Resolution: 1.84→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3848 0 6 140 3994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00993956
X-RAY DIFFRACTIONf_angle_d1.09585413
X-RAY DIFFRACTIONf_chiral_restr0.0627595
X-RAY DIFFRACTIONf_plane_restr0.0087683
X-RAY DIFFRACTIONf_dihedral_angle_d16.96571266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.27071150.232366X-RAY DIFFRACTION89.66
1.89-1.930.26191310.2222529X-RAY DIFFRACTION96.31
1.93-1.990.26181460.2132520X-RAY DIFFRACTION95.52
1.99-2.040.26641450.18652511X-RAY DIFFRACTION95.57
2.04-2.110.22091440.18472533X-RAY DIFFRACTION96.19
2.11-2.190.22541320.18572519X-RAY DIFFRACTION95.98
2.19-2.270.21621330.1932552X-RAY DIFFRACTION95.52
2.27-2.380.24671420.18942521X-RAY DIFFRACTION95.89
2.38-2.50.22311420.17922523X-RAY DIFFRACTION95.69
2.5-2.660.22121190.17212560X-RAY DIFFRACTION96.4
2.66-2.860.20911470.16882515X-RAY DIFFRACTION95.55
2.86-3.150.21911410.17382421X-RAY DIFFRACTION91.34
3.15-3.60.23281290.16512531X-RAY DIFFRACTION95.68
3.6-4.530.15951330.14752521X-RAY DIFFRACTION94.58
4.53-19.480.18721400.17652511X-RAY DIFFRACTION93.08

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