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- PDB-7eys: Complex structure of SptF with Fe, alpha-ketoglutarate, and andic... -

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Basic information

Entry
Database: PDB / ID: 7eys
TitleComplex structure of SptF with Fe, alpha-ketoglutarate, and 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 / metal ion binding / Andiconin D / 2-OXOGLUTARIC ACID / : / 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
Function and homology information
Biological speciesAspergillus sp. (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
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)135,9697
Polymers135,3734
Non-polymers5963
Water8,683482
1
C: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)68,2835
Polymers67,6862
Non-polymers5963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3990 Å2
ΔGint-28 kcal/mol
Surface area21790 Å2
MethodPISA
2
A: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF

B: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF


Theoretical massNumber of molelcules
Total (without water)67,6862
Polymers67,6862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area3230 Å2
ΔGint-24 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.366, 72.227, 77.606
Angle α, β, γ (deg.)81.582, 85.581, 70.243
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: 33843.184 Da / Num. of mol.: 4
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-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#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.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 1.9 Å3/Da / Density % sol: 35.34 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.27 M magnesium chloride, 16% w/v PEG 3350, 1.5% trimethylamine N-oxide dihydrate

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Data collection

DiffractionMean temperature: 283 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: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→47.7 Å / Num. obs: 70547 / % possible obs: 97 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.05 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.8
Reflection shellResolution: 1.95→1.99 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4499 / CC1/2: 0.907

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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: 1.95→47.7 Å / SU ML: 0.2364 / Cross valid method: FREE R-VALUE / σ(F): 1.79 / Phase error: 30.3481
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2682 1996 2.83 %
Rwork0.213 68471 -
obs0.2146 70467 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.69 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8589 0 40 482 9111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00498906
X-RAY DIFFRACTIONf_angle_d0.691312149
X-RAY DIFFRACTIONf_chiral_restr0.04451281
X-RAY DIFFRACTIONf_plane_restr0.00461590
X-RAY DIFFRACTIONf_dihedral_angle_d15.46413340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.32661380.27724828X-RAY DIFFRACTION95.57
2-2.050.32871490.25234864X-RAY DIFFRACTION95.91
2.05-2.110.29181450.23824803X-RAY DIFFRACTION96.06
2.11-2.180.30281330.22554895X-RAY DIFFRACTION96.47
2.18-2.260.28191490.22954900X-RAY DIFFRACTION96.65
2.26-2.350.29681410.22054893X-RAY DIFFRACTION96.79
2.35-2.460.31021370.22914855X-RAY DIFFRACTION96.67
2.46-2.590.34461510.23044927X-RAY DIFFRACTION97.15
2.59-2.750.26471390.23074889X-RAY DIFFRACTION97.39
2.75-2.960.25791400.22624850X-RAY DIFFRACTION96.46
2.96-3.260.29581460.21944911X-RAY DIFFRACTION96.88
3.26-3.730.24331480.19774918X-RAY DIFFRACTION98.08
3.73-4.70.20061400.17174962X-RAY DIFFRACTION98.27
4.7-47.70.25381400.20364976X-RAY DIFFRACTION98.16

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