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- PDB-7enb: iron and alpha-ketoglutarate-dependent endoperoxidase NvfI with d... -

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Basic information

Entry
Database: PDB / ID: 7enb
Titleiron and alpha-ketoglutarate-dependent endoperoxidase NvfI with different conformation
ComponentsNvfI
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 16, 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

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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)68,7717
Polymers67,9182
Non-polymers8525
Water4,972276
1
A: NvfI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6094
Polymers33,9591
Non-polymers6503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area12830 Å2
MethodPISA
2
B: NvfI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1623
Polymers33,9591
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.747, 79.298, 154.524
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


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-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
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#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.: 276 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 50 mM HEPES pH 7.5, containing 20% PEG3350, 20 mM alpha-KG, 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→47.85 Å / Num. obs: 26939 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 28.27 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.178 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2619 / CC1/2: 0.729

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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→45.62 Å / SU ML: 0.2549 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 2000 7.44 %
Rwork0.1784 24881 -
obs0.1826 26881 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.99 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 54 276 4754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424626
X-RAY DIFFRACTIONf_angle_d0.68536315
X-RAY DIFFRACTIONf_chiral_restr0.0481668
X-RAY DIFFRACTIONf_plane_restr0.0059833
X-RAY DIFFRACTIONf_dihedral_angle_d10.0359706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.29551410.22331747X-RAY DIFFRACTION100
2.36-2.420.29311390.22331743X-RAY DIFFRACTION100
2.42-2.490.2511410.22441746X-RAY DIFFRACTION100
2.49-2.570.27221410.211757X-RAY DIFFRACTION100
2.57-2.660.2991410.20321753X-RAY DIFFRACTION100
2.66-2.770.25411400.20361741X-RAY DIFFRACTION99.95
2.77-2.90.2851420.2011761X-RAY DIFFRACTION100
2.9-3.050.2571410.18761768X-RAY DIFFRACTION99.95
3.05-3.240.22421410.18781752X-RAY DIFFRACTION99.95
3.24-3.490.24791430.1781777X-RAY DIFFRACTION100
3.49-3.840.20921440.16361790X-RAY DIFFRACTION100
3.84-4.40.21451450.14841806X-RAY DIFFRACTION99.85
4.4-5.540.18961460.14441812X-RAY DIFFRACTION100
5.54-45.620.2031550.17061928X-RAY DIFFRACTION99.71

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