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- PDB-9dqp: Crystal structure of apo-HrmJ from Streptomyces sp. Ag109_G2-6 (H... -

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Basic information

Entry
Database: PDB / ID: 9dqp
TitleCrystal structure of apo-HrmJ from Streptomyces sp. Ag109_G2-6 (HrmJ-ssa)
Components2OG-Fe dioxygenase family protein
KeywordsOXIDOREDUCTASE / hydroxylase / non-heme iron 2OG enzyme
Function / homology2OG-Fe dioxygenase / 2OG-Fe dioxygenase / dioxygenase activity / : / THIOCYANATE ION / 2OG-Fe dioxygenase family protein
Function and homology information
Biological speciesStreptomyces sp. Ag109_G2-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)58,9787
Polymers58,6922
Non-polymers2865
Water6,774376
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)97.052, 42.931, 126.758
Angle α, β, γ (deg.)90.000, 107.026, 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
Components on special symmetry positions
IDModelComponents
11B-538-

HOH

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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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.15 Å3/Da / Density % sol: 42.82 %
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: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 35459 / % possible obs: 96.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 17.64 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.084 / Net I/σ(I): 15.4
Reflection shellResolution: 1.95→1.98 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1751 / CC1/2: 0.901 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→38.96 Å / SU ML: 0.2203 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.5079
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2514 1626 4.98 %
Rwork0.1981 31034 -
obs0.2007 32660 88.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.28 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 14 376 4084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733849
X-RAY DIFFRACTIONf_angle_d0.90575219
X-RAY DIFFRACTIONf_chiral_restr0.0594542
X-RAY DIFFRACTIONf_plane_restr0.0094705
X-RAY DIFFRACTIONf_dihedral_angle_d15.81571462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.3498790.25291539X-RAY DIFFRACTION53.99
2.01-2.070.2845890.24542025X-RAY DIFFRACTION69.4
2.07-2.150.2991170.2392202X-RAY DIFFRACTION76.01
2.15-2.230.27311550.21842723X-RAY DIFFRACTION94.95
2.23-2.340.29531620.20922816X-RAY DIFFRACTION98.28
2.34-2.460.27711530.22022837X-RAY DIFFRACTION97.84
2.46-2.610.31091510.21562827X-RAY DIFFRACTION97.58
2.61-2.810.27221500.21362801X-RAY DIFFRACTION96.03
2.81-3.10.24341370.20532675X-RAY DIFFRACTION91.21
3.1-3.540.2361540.19082806X-RAY DIFFRACTION96.26
3.55-4.460.19211460.1552863X-RAY DIFFRACTION97.5
4.47-38.960.22631330.18232920X-RAY DIFFRACTION95.41

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