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- PDB-9fnr: Artificial metalloenzyme with a nickel-based 1,10-phenanthroline ... -

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Basic information

Entry
Database: PDB / ID: 9fnr
TitleArtificial metalloenzyme with a nickel-based 1,10-phenanthroline cofactor and streptavidin S112V mutant
ComponentsStreptavidin
KeywordsMETAL BINDING PROTEIN / Artificial metalloenzyme / nickel
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: 1.64 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 10, 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

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2513
Polymers16,5811
Non-polymers6702
Water54030
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,00612
Polymers66,3244
Non-polymers2,6818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area9270 Å2
ΔGint-57 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.100, 57.100, 172.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-310-

HOH

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Components

#1: Protein Streptavidin


Mass: 16581.086 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-A1ICD / N-methyl-N-[(4,4,6,6-tetrahydroxy-4,6-dioxido-1,3,3a,5,6a-tetrahydrothien[3,4-d]imidazol-4-ium-2-yl)methyl]-5-(2,4,4-trihydroxy-2-keto-3,3a,5,6-tetrahydro-1H-thien[3,4-d]imidazol-4-ium-6-yl


Mass: 574.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29N5NiO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1.6M Magnesium sulfate heptahydrate,0.1M HEPES 7.2, 6% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.64→43.05 Å / Num. obs: 31995 / % possible obs: 96.2 % / Redundancy: 18.25 % / Biso Wilson estimate: 32.12 Å2 / CC1/2: 1 / Rrim(I) all: 0.054 / Net I/σ(I): 27.36
Reflection shellResolution: 1.64→1.73 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4478 / CC1/2: 0.512 / Rrim(I) all: 1.39 / % possible all: 79.2

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Processing

Software
NameVersionClassification
PHENIXdev_5246refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→43.05 Å / SU ML: 0.2029 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.0845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2057 1582 5.01 %
Rwork0.1621 29964 -
obs0.1643 31546 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.32 Å2
Refinement stepCycle: LAST / Resolution: 1.64→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms929 0 42 30 1001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0102999
X-RAY DIFFRACTIONf_angle_d1.77251379
X-RAY DIFFRACTIONf_chiral_restr0.0595148
X-RAY DIFFRACTIONf_plane_restr0.0074168
X-RAY DIFFRACTIONf_dihedral_angle_d18.9284317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.690.3706840.3191685X-RAY DIFFRACTION59.1
1.69-1.760.28791350.25952560X-RAY DIFFRACTION88.3
1.76-1.830.25441430.22562761X-RAY DIFFRACTION96.83
1.83-1.910.25531520.18642850X-RAY DIFFRACTION99.34
1.91-2.010.23331520.17362863X-RAY DIFFRACTION100
2.01-2.130.19751510.14532874X-RAY DIFFRACTION100
2.14-2.30.21011500.14962877X-RAY DIFFRACTION99.97
2.3-2.530.2361570.1962865X-RAY DIFFRACTION100
2.53-2.90.22671500.17142879X-RAY DIFFRACTION100
2.9-3.650.1861520.15822870X-RAY DIFFRACTION99.97
3.65-43.050.18551560.14382880X-RAY DIFFRACTION100

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