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- PDB-7fcb: SptF 9 residues truncated mutant -

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Basic information

Entry
Database: PDB / ID: 7fcb
TitleSptF 9 residues truncated mutant
Components2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
KeywordsOXIDOREDUCTASE / SptF / alpha-ketoglutarate dependent oxygenase / biosynthesis
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / : / N-OXALYLGLYCINE / 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
Function and homology information
Biological speciesAspergillus sp. (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHui, T. / 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
DepositionJul 14, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9313
Polymers32,7281
Non-polymers2032
Water4,882271
1
C: 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)65,8626
Polymers65,4562
Non-polymers4064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4650 Å2
ΔGint-54 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.210, 52.316, 57.784
Angle α, β, γ (deg.)90.000, 99.440, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-594-

HOH

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Components

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


Mass: 32727.922 Da / Num. of mol.: 1
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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium formate (pH 7.0), 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: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→45.1 Å / Num. obs: 52223 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 12.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2577 / CC1/2: 0.854 / % possible all: 99.5

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Processing

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

7eyr


Resolution: 1.4→45.1 Å / SU ML: 0.1129 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.6536
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1955 2000 3.83 %
Rwork0.169 50217 -
obs0.17 52217 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.1 Å2
Refinement stepCycle: LAST / Resolution: 1.4→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 11 271 2465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582268
X-RAY DIFFRACTIONf_angle_d0.94873087
X-RAY DIFFRACTIONf_chiral_restr0.0824327
X-RAY DIFFRACTIONf_plane_restr0.0087405
X-RAY DIFFRACTIONf_dihedral_angle_d6.1654298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.21081420.20013589X-RAY DIFFRACTION99.31
1.44-1.470.22411420.19613528X-RAY DIFFRACTION99.32
1.47-1.520.20131420.18113559X-RAY DIFFRACTION99.49
1.52-1.570.18491420.17273589X-RAY DIFFRACTION99.63
1.57-1.620.20341420.17483577X-RAY DIFFRACTION99.79
1.62-1.690.22071420.17993572X-RAY DIFFRACTION99.7
1.69-1.760.2051420.17753565X-RAY DIFFRACTION99.89
1.76-1.860.20751440.16963605X-RAY DIFFRACTION99.79
1.86-1.970.17021420.16483554X-RAY DIFFRACTION99.73
1.97-2.130.19221430.16283583X-RAY DIFFRACTION99.73
2.13-2.340.17971430.17033586X-RAY DIFFRACTION99.63
2.34-2.680.20331430.17283612X-RAY DIFFRACTION99.79
2.68-3.370.19121440.16833612X-RAY DIFFRACTION99.79
3.37-45.10.19631470.15743686X-RAY DIFFRACTION99.4

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