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- PDB-7emz: iron and alpha-ketoglutarate-dependent endoperoxidase NvfI W199F ... -

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Basic information

Entry
Database: PDB / ID: 7emz
Titleiron and alpha-ketoglutarate-dependent endoperoxidase NvfI W199F variant
ComponentsNvfI W199F
KeywordsOXIDOREDUCTASE / Novofumigatonin / endoperoxidase
Function / homology: / Chem-H3X / N-OXALYLGLYCINE
Function and homology information
Biological speciesAspergillus novofumigatus IBT 16806 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMori, 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
DepositionApr 15, 2021Deposition 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NvfI W199F
B: NvfI W199F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6937
Polymers67,8402
Non-polymers8525
Water4,702261
1
A: NvfI W199F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5704
Polymers33,9201
Non-polymers6503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-11 kcal/mol
Surface area12810 Å2
MethodPISA
2
B: NvfI W199F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1233
Polymers33,9201
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.915, 81.112, 151.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein NvfI W199F


Mass: 33920.129 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-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / 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.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 50 mM HEPES pH 7.5, 20% PEG3350, 20 mM alpha-ketoglutarate, 100 mM NaSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.07 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.3→47.92 Å / Num. obs: 27142 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 27.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.136 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 3 / Num. unique obs: 2614 / CC1/2: 0.816 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DE2

7de2


Resolution: 2.3→45.69 Å / SU ML: 0.2749 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2479 2000 7.38 %
Rwork0.1932 25083 -
obs0.1971 27083 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.55 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 54 261 4706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284576
X-RAY DIFFRACTIONf_angle_d0.57516243
X-RAY DIFFRACTIONf_chiral_restr0.0459663
X-RAY DIFFRACTIONf_plane_restr0.0041825
X-RAY DIFFRACTIONf_dihedral_angle_d16.20211756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.2831400.23271750X-RAY DIFFRACTION99.95
2.36-2.420.30211410.22521773X-RAY DIFFRACTION100
2.42-2.490.27891390.23581748X-RAY DIFFRACTION99.95
2.49-2.570.34421400.23911755X-RAY DIFFRACTION100
2.57-2.660.27921420.22621777X-RAY DIFFRACTION100
2.66-2.770.26811400.20691761X-RAY DIFFRACTION100
2.77-2.90.27141430.20811779X-RAY DIFFRACTION100
2.9-3.050.26461400.21561769X-RAY DIFFRACTION99.95
3.05-3.240.26571440.20581796X-RAY DIFFRACTION100
3.24-3.490.24481420.19431786X-RAY DIFFRACTION100
3.49-3.840.25521430.17561791X-RAY DIFFRACTION100
3.84-4.40.22281440.15581814X-RAY DIFFRACTION100
4.4-5.540.16131470.16371840X-RAY DIFFRACTION100
5.54-45.690.24281550.18581944X-RAY DIFFRACTION99.81

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