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- PDB-6s50: scdSav(SARK)mv2 - Engineering Single-Chain Dimeric Streptavidin a... -

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Basic information

Entry
Database: PDB / ID: 6s50
TitlescdSav(SARK)mv2 - Engineering Single-Chain Dimeric Streptavidin as Host for Artificial Metalloenzymes
ComponentsStreptavidin
Keywordsbiotin-binding protein / Artificial Transfer Hydrogenase / Beta Barrel / Streptavidin / TRANSPORT 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
Chem-4IR / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRebelein, J.G.
Funding support Switzerland, Germany, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation200020_182046 Switzerland
European Research CouncilDrEAM
Swiss National Science FoundationNCCR MSE Switzerland
European Molecular Biology OrganizationALTF 194-2017 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Breaking Symmetry: Engineering Single-Chain Dimeric Streptavidin as Host for Artificial Metalloenzymes.
Authors: Wu, S. / Zhou, Y. / Rebelein, J.G. / Kuhn, M. / Mallin, H. / Zhao, J. / Igareta, N.V. / Ward, T.R.
History
DepositionJun 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,80213
Polymers69,9242
Non-polymers3,87911
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-29 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.879, 57.771, 57.645
Angle α, β, γ (deg.)90.00, 108.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Streptavidin /


Mass: 34961.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical
ChemComp-4IR / {N-(4-{[2-(amino-kappaN)ethyl]sulfamoyl-kappaN}phenyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide}(chloro)[(1,2,3,4,5-eta)-1,2,3,4,5-pentamethylcyclopentadienyl]iridium(III) / N-(4-{[(2-AMINOETHYL)AMINO]SULFONYL}PHENYL)-5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANAMIDE-(1,2,3,4,5,6-ETA)-PENTAMETHYLCYCLOHEXYL-CHLORO-IRIDIUM(III)


Mass: 807.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H45ClIrN5O4S2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 2 M (NH4)2SO4, 0.1 M Na-Acetate, pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40.99 Å / Num. obs: 38602 / % possible obs: 99.89 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.0678 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.071 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.3786 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 3856 / CC1/2: 0.78 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PK2

3pk2


Resolution: 2→40.99 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.88
RfactorNum. reflection% reflection
Rfree0.2078 2544 3.57 %
Rwork0.1855 --
obs0.1863 38591 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 205 129 4017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144039
X-RAY DIFFRACTIONf_angle_d2.1945674
X-RAY DIFFRACTIONf_dihedral_angle_d10.4962793
X-RAY DIFFRACTIONf_chiral_restr0.077587
X-RAY DIFFRACTIONf_plane_restr0.007673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03850.40181340.28713710X-RAY DIFFRACTION90
2.0385-2.08010.27281300.24613609X-RAY DIFFRACTION91
2.0801-2.12530.27391450.22563825X-RAY DIFFRACTION94
2.1253-2.17470.22471380.20523957X-RAY DIFFRACTION95
2.1747-2.22910.23651420.20313878X-RAY DIFFRACTION95
2.2291-2.28940.231440.20023866X-RAY DIFFRACTION95
2.2894-2.35680.24191440.19823845X-RAY DIFFRACTION95
2.3568-2.43280.29061320.19043957X-RAY DIFFRACTION95
2.4328-2.51980.25831530.19983911X-RAY DIFFRACTION96
2.5198-2.62060.2251500.18573908X-RAY DIFFRACTION96
2.6206-2.73990.20531360.19063900X-RAY DIFFRACTION95
2.7399-2.88430.25291520.18223888X-RAY DIFFRACTION96
2.8843-3.06490.221400.18153857X-RAY DIFFRACTION95
3.0649-3.30150.25261480.17093778X-RAY DIFFRACTION93
3.3015-3.63350.1781330.16843755X-RAY DIFFRACTION92
3.6335-4.15890.18011210.16173726X-RAY DIFFRACTION90
4.1589-5.23810.14811380.1463641X-RAY DIFFRACTION90
5.2381-41.00340.1771640.22833608X-RAY DIFFRACTION89

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