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- PDB-7eyu: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF-N65T mutan... -

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Basic information

Entry
Database: PDB / ID: 7eyu
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF-N65T mutant with andiconin D
Components2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
KeywordsOXIDOREDUCTASE / alpha-ketoglutarate dependent dioxygenase / meroterpenoid
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / Andiconin D / : / N-OXALYLGLYCINE / 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
Function and homology information
Biological speciesAspergillus sp. (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTao, H. / Mori, T. / Abe, I.
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,3146
Polymers67,6602
Non-polymers6534
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-49 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.813, 50.583, 71.982
Angle α, β, γ (deg.)109.107, 91.294, 112.859
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: 33830.184 Da / Num. of mol.: 2 / Mutation: N65T
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 / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Chemical ChemComp-0CC / Andiconin D


Mass: 394.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium formate dehydrate, 20% w/v PEG 3350

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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 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→44.6 Å / Num. obs: 31258 / % possible obs: 96.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 12.15 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.176 / Net I/σ(I): 7.1
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2440 / CC1/2: 0.893 / % possible all: 95.7

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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: 2.05→27.85 Å / SU ML: 0.2949 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 31.0785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.278 2013 6.45 %
Rwork0.2409 29207 -
obs0.2433 31220 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.86 Å2
Refinement stepCycle: LAST / Resolution: 2.05→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4303 0 41 293 4637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00294482
X-RAY DIFFRACTIONf_angle_d0.63356122
X-RAY DIFFRACTIONf_chiral_restr0.0416644
X-RAY DIFFRACTIONf_plane_restr0.0047798
X-RAY DIFFRACTIONf_dihedral_angle_d14.77041730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.35641420.28872081X-RAY DIFFRACTION95.65
2.1-2.160.36781360.2642098X-RAY DIFFRACTION96.5
2.16-2.220.29271560.27022115X-RAY DIFFRACTION96.89
2.22-2.290.3461420.26812087X-RAY DIFFRACTION96.37
2.29-2.380.32111460.26362097X-RAY DIFFRACTION96.43
2.38-2.470.3211370.282069X-RAY DIFFRACTION96.54
2.47-2.580.32721470.26732111X-RAY DIFFRACTION96.99
2.58-2.720.27421460.25792097X-RAY DIFFRACTION96.85
2.72-2.890.30181480.26332110X-RAY DIFFRACTION96.29
2.89-3.110.27461410.25512088X-RAY DIFFRACTION96.29
3.11-3.420.27751440.2392057X-RAY DIFFRACTION95.45
3.42-3.920.24411450.21332042X-RAY DIFFRACTION93.42
3.92-4.930.18931390.17612076X-RAY DIFFRACTION96.1
4.93-27.850.22191440.20212079X-RAY DIFFRACTION95.57

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