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- PDB-7de2: iron and alpha-ketoglutarate-dependent endoperoxidase NvfI -

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Basic information

Entry
Database: PDB / ID: 7de2
Titleiron and alpha-ketoglutarate-dependent endoperoxidase NvfI
ComponentsNvfI
KeywordsOXIDOREDUCTASE / Novofumigatonin / endoperoxidase / iron and alpha-ketoglutarate-dependent enzyme
Function / homology2-OXOGLUTARIC ACID / : / Chem-H3X
Function and homology information
Biological speciesAspergillus novofumigatus IBT 16806 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhai, R. / Mori, T. / Abe, I.
CitationJournal: Nat Commun / Year: 2021
Title: Molecular insights into the endoperoxide formation by Fe(II)/ alpha-KG-dependent oxygenase NvfI.
Authors: Mori, T. / Zhai, R. / Ushimaru, R. / Matsuda, Y. / Abe, I.
History
DepositionNov 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NvfI
B: NvfI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7697
Polymers67,9182
Non-polymers8505
Water7,584421
1
A: NvfI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6084
Polymers33,9591
Non-polymers6493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-11 kcal/mol
Surface area12960 Å2
MethodPISA
2
B: NvfI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1613
Polymers33,9591
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-7 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.286, 48.337, 79.638
Angle α, β, γ (deg.)90.000, 101.039, 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

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Components

#1: Protein NvfI


Mass: 33959.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus novofumigatus IBT 16806 (mold)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-H3X / methyl (3'~{a}~{R},4'~{S},5'~{S},5~{a}~{S},6~{S},7~{S},9~{a}~{R})-1,1,3'~{a},4',5~{a},7,7'-heptamethyl-3,6'-bis(oxidanylidene)spiro[4,5,7,8,9,9~{a}-hexahydrobenzo[c]oxepine-6,2'-4,5-dihydro-3~{H}-1-benzofuran]-5'-carboxylate


Mass: 446.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H38O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE / FE (III) 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


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 50 mM Tris-HCl pH 7.0, 20% PEG3350, 20 mM alpha-ketoglutarate, 200 mM NaSCN, and 2 mM DTT

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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 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.13 Å / Num. obs: 46701 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 20.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Net I/σ(I): 11.1
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 3 / Num. unique obs: 3022 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.08 Å / SU ML: 0.1697 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.15
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.193 2325 4.98 %
Rwork0.1719 44343 -
obs0.1729 46668 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.47 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 54 421 4894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914607
X-RAY DIFFRACTIONf_angle_d1.24096286
X-RAY DIFFRACTIONf_chiral_restr0.0722665
X-RAY DIFFRACTIONf_plane_restr0.0086828
X-RAY DIFFRACTIONf_dihedral_angle_d21.4571768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.27041180.21992620X-RAY DIFFRACTION99.96
1.94-1.980.26021150.19892590X-RAY DIFFRACTION100
1.98-2.030.2061520.19552577X-RAY DIFFRACTION99.93
2.03-2.080.22451190.19082579X-RAY DIFFRACTION100
2.08-2.130.23031380.18172591X-RAY DIFFRACTION100
2.13-2.20.23761400.17832617X-RAY DIFFRACTION99.93
2.2-2.270.19581280.17532586X-RAY DIFFRACTION100
2.27-2.350.21681450.17872601X-RAY DIFFRACTION100
2.35-2.440.19341250.17892582X-RAY DIFFRACTION99.96
2.44-2.550.19681290.17682629X-RAY DIFFRACTION100
2.55-2.690.20191580.17522571X-RAY DIFFRACTION99.96
2.69-2.860.21351560.17452594X-RAY DIFFRACTION100
2.86-3.080.17821340.17732612X-RAY DIFFRACTION100
3.08-3.390.20751530.16882600X-RAY DIFFRACTION100
3.39-3.880.15571290.16062638X-RAY DIFFRACTION100
3.88-4.880.15211570.14232647X-RAY DIFFRACTION99.96
4.88-39.080.18891290.17462709X-RAY DIFFRACTION99.09

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