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- PDB-9j0j: The crystal structure of Fe/2OG-dependent oxygenase DfmD -

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Basic information

Entry
Database: PDB / ID: 9j0j
TitleThe crystal structure of Fe/2OG-dependent oxygenase DfmD
ComponentsFe/2OG-dependent oxygenase DfmD
KeywordsOXIDOREDUCTASE / oxygenase / DfmD
Function / homology:
Function and homology information
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWang, L. / Chen, J. / Zhou, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: An Alternative Mechanism for C-C Desaturation Underscores a Dual-Controlled Mechanism for the Fate of Radical Intermediate in Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenase DfmD.
Authors: Zhang, X. / Wang, L. / Liu, J. / Chen, T.Y. / Yan, S. / Chang, W.C. / Shaik, S. / Zhou, J. / Wang, B.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fe/2OG-dependent oxygenase DfmD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4358
Polymers45,8541
Non-polymers5827
Water90150
1
A: Fe/2OG-dependent oxygenase DfmD
hetero molecules

A: Fe/2OG-dependent oxygenase DfmD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,87116
Polymers91,7072
Non-polymers1,16314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area8660 Å2
ΔGint-50 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.316, 110.316, 88.835
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Fe/2OG-dependent oxygenase DfmD


Mass: 45853.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal truncation of 5 amino acids / Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.4 Å3/Da / Density % sol: 69.35 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M K/Na tartrate, 0.1 M CHES/NaOH pH 9.5, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 14802 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 49.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 43.6
Reflection shellResolution: 2.85→2.9 Å / Rmerge(I) obs: 1.288 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1371 / CC1/2: 0.836 / Rpim(I) all: 0.291 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→32.53 Å / SU ML: 0.2435 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9795
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2254 731 4.93 %
Rwork0.1879 14095 -
obs0.1897 14792 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.44 Å2
Refinement stepCycle: LAST / Resolution: 2.85→32.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 0 32 51 2803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862819
X-RAY DIFFRACTIONf_angle_d0.94573813
X-RAY DIFFRACTIONf_chiral_restr0.0491391
X-RAY DIFFRACTIONf_plane_restr0.0079495
X-RAY DIFFRACTIONf_dihedral_angle_d15.45251002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.070.28181440.2352689X-RAY DIFFRACTION95.77
3.07-3.370.2591410.20642802X-RAY DIFFRACTION99.8
3.37-3.860.23611430.19042809X-RAY DIFFRACTION99.7
3.86-4.860.19991330.16442865X-RAY DIFFRACTION99.83
4.86-32.530.20751700.18442930X-RAY DIFFRACTION99.71

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