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

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Basic information

Entry
Database: PDB / ID: 7eyt
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF with andilesin C and NOG
Components2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
KeywordsOXIDOREDUCTASE / alpha-ketoglutarate dependent dioxygenase / meroterpenoid
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / Andilesin C / : / N-OXALYLGLYCINE / 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
Function and homology information
Biological speciesAspergillus sp. (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)136,15610
Polymers135,3734
Non-polymers7836
Water7,981443
1
C: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
B: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3586
Polymers67,6862
Non-polymers6714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-54 kcal/mol
Surface area22010 Å2
MethodPISA
2
A: 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF
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
Buried area3600 Å2
ΔGint-48 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.054, 72.557, 78.826
Angle α, β, γ (deg.)81.739, 84.189, 70.229
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-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#3: Chemical ChemComp-0I3 / Andilesin C


Mass: 412.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H32O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 1.97 Å3/Da / Density % sol: 37.45 %
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: 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: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.42 Å / Num. obs: 56771 / % possible obs: 94.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 21.87 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.138 / Net I/σ(I): 5.7
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4484 / CC1/2: 0.906 / % possible all: 95.1

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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→48.42 Å / SU ML: 0.3021 / Cross valid method: FREE R-VALUE / σ(F): 0.83 / Phase error: 32.6001
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.286 1995 3.52 %
Rwork0.2361 54656 -
obs0.2378 56651 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8524 0 44 443 9011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00258837
X-RAY DIFFRACTIONf_angle_d0.594812064
X-RAY DIFFRACTIONf_chiral_restr0.03971287
X-RAY DIFFRACTIONf_plane_restr0.00431573
X-RAY DIFFRACTIONf_dihedral_angle_d16.74383272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.27811450.24393976X-RAY DIFFRACTION95.09
2.15-2.210.30681440.26513932X-RAY DIFFRACTION94.97
2.21-2.280.36161440.26313944X-RAY DIFFRACTION94.72
2.28-2.350.31991410.26943859X-RAY DIFFRACTION93.5
2.35-2.430.32081410.27333847X-RAY DIFFRACTION92.92
2.43-2.530.37281350.28363721X-RAY DIFFRACTION89.3
2.53-2.650.36521380.29153734X-RAY DIFFRACTION90.34
2.65-2.790.3561370.27253801X-RAY DIFFRACTION91.01
2.79-2.960.28241440.25563931X-RAY DIFFRACTION95.19
2.96-3.190.32381480.24144040X-RAY DIFFRACTION97.46
3.19-3.510.24771470.2284010X-RAY DIFFRACTION97.17
3.51-4.020.23541460.1964000X-RAY DIFFRACTION96.37
4.02-5.060.23121450.18483959X-RAY DIFFRACTION95.31
5.06-48.420.26051400.23043902X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.247412458190.208884075248-0.08056662905891.96221994671-0.04184157282470.4088460352460.132855906393-0.08326446290470.141160955267-0.0093291038631-0.0170279945156-0.126054897926-0.218099682422-0.00260542530494-0.1200890979010.39610960457-0.0006893050850960.06256828572080.182107763753-0.03622027861910.155384646233.6160269763760.170870821233.6138130037
21.052756237910.230005806912-0.1158387144142.31521470540.3618859590371.672162451660.1207986387080.05933766358420.0532005591266-0.1768884834140.0316339221631-0.125440544376-0.217094004122-0.0694048361809-0.1418787613650.1524427790680.04678347074110.03043102494590.1353036716220.01112440559170.141280201587-17.844581647764.23980741173.7140758873
32.21154653785-0.255793360084-0.4110228302313.52055192355-0.06466767155862.26977645452-0.06876121779160.0922601510767-0.0958746760588-0.2531233459830.0472589582283-0.2497675350160.1388963005870.1498404310150.0211773365240.198033431902-0.0002290654374230.02299131799670.137757450609-0.02073916876560.1329031419055.649292922425.823896743333.209510995
41.78148203552-0.183022911695-0.6155357894323.867241084260.04625684474392.07707132523-0.0783359507797-0.00422497812693-0.119251496594-0.1027292899110.0080943926652-0.12060823780.251529125991-0.02953495061720.068374851840.1367689269550.0200331986547-0.03680739797050.1544661959520.02128616937850.151207140804-15.148352382130.135604316472.9797447802
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 6 through 280)BE6 - 2801 - 267
22(chain 'D' and resid 5 through 288)DF5 - 2881 - 276
33(chain 'C' and resid 2 through 278)CA2 - 2781 - 277
44(chain 'A' and resid 2 through 278)AD2 - 2781 - 258

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