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- PDB-7eyw: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF with terre... -

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Basic information

Entry
Database: PDB / ID: 7eyw
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF with terretonin C
Components2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
KeywordsOXIDOREDUCTASE / alpha-ketoglutarate dependent dioxygenase / meroterpenoid
Function / homology
Function and homology information


biosynthetic process / dioxygenase activity / metal ion binding
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Terretonin C / : / N-OXALYLGLYCINE / 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
Similarity search - Component
Biological speciesAspergillus sp. (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTao, H. / Mori, T. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Molecular insights into the unusually promiscuous and catalytically versatile Fe(II)/ alpha-ketoglutarate-dependent oxygenase SptF.
Authors: Tao, H. / Mori, T. / Chen, H. / Lyu, S. / Nonoyama, A. / Lee, S. / Abe, I.
History
DepositionJun 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
A: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
B: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
D: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,55113
Polymers135,3094
Non-polymers1,2429
Water6,774376
1
B: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
hetero molecules

C: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4917
Polymers67,6542
Non-polymers8365
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area4530 Å2
ΔGint-51 kcal/mol
Surface area22490 Å2
MethodPISA
2
A: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
hetero molecules

D: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0606
Polymers67,6542
Non-polymers4064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4460 Å2
ΔGint-54 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.651, 72.281, 78.455
Angle α, β, γ (deg.)81.929, 84.880, 70.354
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
2-oxoglutarate/Fe(II)-dependent dioxygenase SptF


Mass: 33827.184 Da / Num. of mol.: 4 / Mutation: S114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus sp. (mold) / Gene: sptF / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6J4CX17
#2: Chemical
ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H5NO5
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-0IP / Terretonin C


Mass: 430.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.54 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.27 M magnesium chloride, 20% w/v PEG 3350, 0.2 M sodium chloride, 1.5% trimethylamine N-oxide dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.07 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.1→48.24 Å / Num. obs: 57878 / % possible obs: 97.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 9566 / CC1/2: 0.871 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EYR

7eyr


Resolution: 2.1→48.24 Å / SU ML: 0.2901 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 29.1052
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2558 1999 3.46 %
Rwork0.2056 55782 -
obs0.2073 57781 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8465 0 75 376 8916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00248793
X-RAY DIFFRACTIONf_angle_d0.566711984
X-RAY DIFFRACTIONf_chiral_restr0.04081261
X-RAY DIFFRACTIONf_plane_restr0.00471578
X-RAY DIFFRACTIONf_dihedral_angle_d16.63463295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.3431420.29613958X-RAY DIFFRACTION96.11
2.15-2.210.35491400.28083899X-RAY DIFFRACTION96.37
2.21-2.280.35681430.26853996X-RAY DIFFRACTION96.71
2.28-2.350.30831410.25343950X-RAY DIFFRACTION96.44
2.35-2.430.30421410.24233925X-RAY DIFFRACTION96.81
2.43-2.530.28041430.23224007X-RAY DIFFRACTION97.24
2.53-2.650.26981420.22763947X-RAY DIFFRACTION97.26
2.65-2.790.29091450.234026X-RAY DIFFRACTION97.66
2.79-2.960.28851420.22473985X-RAY DIFFRACTION97.84
2.96-3.190.3031440.21173998X-RAY DIFFRACTION98.04
3.19-3.510.27241430.20363980X-RAY DIFFRACTION97.59
3.51-4.020.20531440.17224040X-RAY DIFFRACTION98.17
4.02-5.060.17721440.15234042X-RAY DIFFRACTION98.94
5.06-48.240.22441450.18734029X-RAY DIFFRACTION98.44

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