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

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Basic information

Entry
Database: PDB / ID: 9dqq
TitleCrystal structure of HrmJ from Streptomyces sp. Ag109_G2-6 (HrmJ-ssa) complexed with ferric iron(III) and 2-oxoglutarate
Components2OG-Fe dioxygenase family protein
KeywordsOXIDOREDUCTASE / hydroxylase / non-heme iron 2OG enzyme
Function / homology2OG-Fe dioxygenase / 2OG-Fe dioxygenase / dioxygenase activity / 2-OXOGLUTARIC ACID / : / 2OG-Fe dioxygenase family protein
Function and homology information
Biological speciesStreptomyces sp. Ag109_G2-6 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 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
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)59,1517
Polymers58,6922
Non-polymers4605
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.871, 43.616, 126.201
Angle α, β, γ (deg.)90.000, 106.949, 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-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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 43.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.22 M KSCN, 26% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Aug 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.45→17.68 Å / Num. obs: 18054 / % possible obs: 96 % / Redundancy: 6.7 % / Biso Wilson estimate: 42.99 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.9
Reflection shellResolution: 2.45→2.55 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2016 / CC1/2: 0.767

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→17.68 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2796 901 4.99 %
Rwork0.2073 17144 -
obs0.211 18045 95.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.89 Å2
Refinement stepCycle: LAST / Resolution: 2.45→17.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 23 116 3708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733709
X-RAY DIFFRACTIONf_angle_d0.88275028
X-RAY DIFFRACTIONf_chiral_restr0.0509523
X-RAY DIFFRACTIONf_plane_restr0.0077681
X-RAY DIFFRACTIONf_dihedral_angle_d15.45441406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.60.29561340.24592795X-RAY DIFFRACTION94.48
2.6-2.80.3111330.24052849X-RAY DIFFRACTION95.12
2.8-3.080.31581720.23382806X-RAY DIFFRACTION95.66
3.08-3.530.30411470.21392868X-RAY DIFFRACTION96.3
3.53-4.430.26291570.18142907X-RAY DIFFRACTION96.75
4.43-17.680.25681580.20112919X-RAY DIFFRACTION95.38

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