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

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Basic information

Entry
Database: PDB / ID: 9ffj
TitleArtificial metalloenzyme with a nickel-based 1,10-phenanthroline cofactor and streptavidin N49M-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
: / AMMONIUM ION / DI(HYDROXYETHYL)ETHER / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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
DepositionMay 23, 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)17,7199
Polymers16,5981
Non-polymers1,1218
Water64936
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,87636
Polymers66,3934
Non-polymers4,48332
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 area13600 Å2
ΔGint-113 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.460, 57.460, 172.460
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-84-

ARG

21A-314-

HOH

31A-335-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Streptavidin


Mass: 16598.178 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

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Non-polymers , 6 types, 44 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 11% w/v PEG 8000 0.1M MES 6.0 0.24M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.27→54.51 Å / Num. obs: 37345 / % possible obs: 97.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.044 / Net I/σ(I): 17.2
Reflection shellResolution: 1.27→1.3 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1801 / CC1/2: 0.746 / Rrim(I) all: 0.759

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Processing

Software
NameVersionClassification
PHENIXdev_5246refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→54.51 Å / SU ML: 0.1694 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.0496
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1965 1859 4.98 %
Rwork0.1772 35479 -
obs0.1782 37338 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.76 Å2
Refinement stepCycle: LAST / Resolution: 1.27→54.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 70 36 1015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871136
X-RAY DIFFRACTIONf_angle_d2.2751582
X-RAY DIFFRACTIONf_chiral_restr0.0965160
X-RAY DIFFRACTIONf_plane_restr0.0079191
X-RAY DIFFRACTIONf_dihedral_angle_d18.1177371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.310.33111400.31852711X-RAY DIFFRACTION99.06
1.31-1.350.2871440.26692705X-RAY DIFFRACTION99.34
1.35-1.390.29511320.21792732X-RAY DIFFRACTION99.44
1.39-1.440.23771370.18932772X-RAY DIFFRACTION99.18
1.44-1.50.18631370.17372694X-RAY DIFFRACTION98.47
1.5-1.570.21311360.18712769X-RAY DIFFRACTION98.94
1.57-1.650.24571320.2062734X-RAY DIFFRACTION98.73
1.65-1.750.23831440.18682734X-RAY DIFFRACTION98.29
1.75-1.890.16861180.15542728X-RAY DIFFRACTION97.3
1.89-2.080.16341660.14482721X-RAY DIFFRACTION97.27
2.08-2.380.16321580.1562709X-RAY DIFFRACTION96.66
2.38-30.18341500.17382711X-RAY DIFFRACTION95.18
3-54.510.2021650.18112759X-RAY DIFFRACTION92.09

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