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- PDB-9foa: Artificial photoenzyme with anthraquinone cofactor and wild type ... -

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Basic information

Entry
Database: PDB / ID: 9foa
TitleArtificial photoenzyme with anthraquinone cofactor and wild type streptavidin
ComponentsStreptavidin
KeywordsMETAL BINDING PROTEIN / Artificial photoenzyme / anthraquinone
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: 1.36 Å
AuthorsLau, K. / Wang, W. / Pojer, F. / Larabi, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Artificial Metalloenzymes with Two Catalytic Cofactors for Tandem Abiotic Transformations.
Authors: Wang, W. / Tachibana, R. / Zhang, K. / Lau, K. / Pojer, F. / Ward, T.R. / Hu, X.
History
DepositionJun 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2995
Polymers16,5691
Non-polymers7304
Water1,42379
1
D: Streptavidin
hetero molecules

D: Streptavidin
hetero molecules

D: Streptavidin
hetero molecules

D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,19520
Polymers66,2764
Non-polymers2,91916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area14100 Å2
ΔGint-71 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.490, 57.490, 183.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Components on special symmetry positions
IDModelComponents
11D-308-

HOH

21D-321-

HOH

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Components

#1: Protein Streptavidin


Mass: 16569.031 Da / Num. of mol.: 1
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: Chemical ChemComp-A1ID2 / ~{N}-[4-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]butyl]-9,10-bis(oxidanylidene)anthracene-2-carboxamide


Mass: 449.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium sulfate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.36→54.85 Å / Num. obs: 33304 / % possible obs: 98.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.048 / Net I/σ(I): 16.5
Reflection shellResolution: 1.36→1.379 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1640 / CC1/2: 0.754 / Rrim(I) all: 0.581 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIXdev_5246refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→54.85 Å / SU ML: 0.1269 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.2576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1816 1696 5.09 %
Rwork0.1531 31603 -
obs0.1546 33299 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.85 Å2
Refinement stepCycle: LAST / Resolution: 1.36→54.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 49 79 1043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096987
X-RAY DIFFRACTIONf_angle_d1.10891350
X-RAY DIFFRACTIONf_chiral_restr0.0844145
X-RAY DIFFRACTIONf_plane_restr0.0104177
X-RAY DIFFRACTIONf_dihedral_angle_d12.6123338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.40.25831070.23232639X-RAY DIFFRACTION99.17
1.4-1.440.26331330.19882618X-RAY DIFFRACTION99.46
1.44-1.490.21451390.16912615X-RAY DIFFRACTION99.49
1.49-1.550.19111470.1672625X-RAY DIFFRACTION99.53
1.55-1.620.18021510.1422616X-RAY DIFFRACTION99.6
1.62-1.710.15011570.13022609X-RAY DIFFRACTION99.5
1.71-1.820.16511490.12932646X-RAY DIFFRACTION99.47
1.82-1.960.19381690.13652627X-RAY DIFFRACTION99.25
1.96-2.150.16871440.12792641X-RAY DIFFRACTION98.97
2.15-2.460.17631350.14052637X-RAY DIFFRACTION97.37
2.46-3.10.17941310.15932655X-RAY DIFFRACTION96.74
3.1-54.850.18231340.16342675X-RAY DIFFRACTION91.98

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