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- PDB-9dqr: Crystal structure of HrmJ from Streptomyces sp. Ag109_G2-6 (HrmJ-... -

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Basic information

Entry
Database: PDB / ID: 9dqr
TitleCrystal structure of HrmJ from Streptomyces sp. Ag109_G2-6 (HrmJ-ssa) complexed with vanadyl(IV)-oxo and succinate
Components2OG-Fe dioxygenase family protein
KeywordsOXIDOREDUCTASE / hydroxylase / non-heme iron 2OG enzyme
Function / homology2OG-Fe dioxygenase / 2OG-Fe dioxygenase / dioxygenase activity / SUCCINIC ACID / oxovanadium(2+) / 2OG-Fe dioxygenase family protein
Function and homology information
Biological speciesStreptomyces sp. Ag109_G2-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZheng, Y.-C. / Chang, W.-C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Comparison of a Nonheme Iron Cyclopropanase with a Homologous Hydroxylase Reveals Mechanistic Features Associated with Distinct Reaction Outcomes.
Authors: Zheng, Y.C. / Li, X. / Cha, L. / Paris, J.C. / Michael, C. / Ushimaru, R. / Ogasawara, Y. / Abe, I. / Guo, Y. / Chang, W.C.
History
DepositionSep 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 5, 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: 2OG-Fe dioxygenase family protein
B: 2OG-Fe dioxygenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0626
Polymers58,6922
Non-polymers3704
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.622, 44.668, 126.433
Angle α, β, γ (deg.)90.000, 107.111, 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 2OG-Fe dioxygenase family protein


Mass: 29345.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Ag109_G2-6 (bacteria) / Gene: EDD96_7010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3N4ZHX0
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.176 M KSCN, 20.8% (w/v) PEG 3350, 20 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34947 / % possible obs: 97.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 24.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.8
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1715 / CC1/2: 0.883

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.36 Å / SU ML: 0.1952 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.1768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2107 1773 5.09 %
Rwork0.1759 33068 -
obs0.1777 34841 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.57 Å2
Refinement stepCycle: LAST / Resolution: 2→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 20 349 4099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01323878
X-RAY DIFFRACTIONf_angle_d1.16835255
X-RAY DIFFRACTIONf_chiral_restr0.0804545
X-RAY DIFFRACTIONf_plane_restr0.011714
X-RAY DIFFRACTIONf_dihedral_angle_d15.76591468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.24041400.20062379X-RAY DIFFRACTION92.75
2.06-2.120.29341150.20152499X-RAY DIFFRACTION95.82
2.12-2.190.26341370.19572415X-RAY DIFFRACTION93.82
2.19-2.260.21661420.1922583X-RAY DIFFRACTION98.7
2.26-2.360.22091110.18682604X-RAY DIFFRACTION98.51
2.36-2.460.22441340.18952572X-RAY DIFFRACTION98.9
2.46-2.590.20231510.17692527X-RAY DIFFRACTION98.75
2.59-2.750.20811370.18522565X-RAY DIFFRACTION98.61
2.75-2.970.221490.18522559X-RAY DIFFRACTION98.22
2.97-3.270.21721390.17522448X-RAY DIFFRACTION94.42
3.27-3.740.16621440.16562639X-RAY DIFFRACTION99.71
3.74-4.710.20131220.14482634X-RAY DIFFRACTION99.24
4.71-40.360.20961520.18372644X-RAY DIFFRACTION96.78

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