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- PDB-7eyr: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF apo -

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Basic information

Entry
Database: PDB / ID: 7eyr
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF apo
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
: / 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
Similarity search - Component
Biological speciesAspergillus sp. (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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

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)135,5968
Polymers135,3734
Non-polymers2234
Water8,845491
1
C: 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)67,7984
Polymers67,6862
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area3660 Å2
ΔGint-45 kcal/mol
Surface area23680 Å2
MethodPISA
2
A: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)67,7984
Polymers67,6862
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Buried area3750 Å2
ΔGint-46 kcal/mol
Surface area25410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.570, 72.704, 78.985
Angle α, β, γ (deg.)82.083, 84.949, 70.128
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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 1.96 Å3/Da / Density % sol: 37.14 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.27 M magnesium chloride, 21% w/v PEG 3350, 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 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→48.57 Å / Num. obs: 56744 / % possible obs: 97.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 20.74 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.4
Reflection shellResolution: 2.12→2.18 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4456 / CC1/2: 0.927 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZM2

5zm2


Resolution: 2.12→46.57 Å / SU ML: 0.2703 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 27.9366
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 1996 3.52 %
Rwork0.1955 54652 -
obs0.1975 56648 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.81 Å2
Refinement stepCycle: LAST / Resolution: 2.12→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8762 0 4 491 9257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00269039
X-RAY DIFFRACTIONf_angle_d0.564212314
X-RAY DIFFRACTIONf_chiral_restr0.04051305
X-RAY DIFFRACTIONf_plane_restr0.00481611
X-RAY DIFFRACTIONf_dihedral_angle_d15.4493261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.32671360.26313733X-RAY DIFFRACTION93.61
2.17-2.230.24891410.23093843X-RAY DIFFRACTION96.49
2.23-2.30.2931410.20933884X-RAY DIFFRACTION96.82
2.3-2.370.26051430.20773918X-RAY DIFFRACTION97.04
2.37-2.460.29121430.21633881X-RAY DIFFRACTION97.2
2.46-2.560.28451410.2213904X-RAY DIFFRACTION97.47
2.56-2.670.26181420.21653878X-RAY DIFFRACTION97.53
2.67-2.810.3281440.21483944X-RAY DIFFRACTION97.8
2.81-2.990.29021420.20913892X-RAY DIFFRACTION98.17
2.99-3.220.2171450.19343949X-RAY DIFFRACTION98.34
3.22-3.550.24891440.1893957X-RAY DIFFRACTION98.58
3.55-4.060.23911440.16413972X-RAY DIFFRACTION98.78
4.06-5.110.19221450.15693949X-RAY DIFFRACTION99.13
5.11-46.570.23771450.1943948X-RAY DIFFRACTION98.44

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