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- PDB-9dq1: Crystal structure of HrmJ from Streptomyces sp. CFMR 7 (HrmJ-ssc)... -

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Basic information

Entry
Database: PDB / ID: 9dq1
TitleCrystal structure of HrmJ from Streptomyces sp. CFMR 7 (HrmJ-ssc) complexed with manganese (II), 2-oxoglutarate and 6-nitronorleucine
ComponentsBsmA domain containing protein
KeywordsOXIDOREDUCTASE / cyclopropanase
Function / homology2OG-Fe dioxygenase / 2OG-Fe dioxygenase / dioxygenase activity / 6-nitro-L-norleucine / 2-OXOGLUTARIC ACID / IODIDE ION / : / BsmA domain containing protein
Function and homology information
Biological speciesStreptomyces sp. CFMR 7 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZheng, Y.-C. / Swartz, P. / 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 23, 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: BsmA domain containing protein
B: BsmA domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,06219
Polymers52,9972
Non-polymers2,06517
Water9,620534
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.342, 74.971, 87.295
Angle α, β, γ (deg.)90.000, 90.032, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BsmA domain containing protein


Mass: 26498.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CFMR 7 (bacteria) / Gene: ABE83_05625 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M5J3M0

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Non-polymers , 7 types, 551 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-6HN / 6-nitro-L-norleucine


Type: L-peptide linking / Mass: 176.170 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaI; 0.1 M bis-tris propane, pH 6.5; 20% (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: Feb 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.9→17.73 Å / Num. obs: 45410 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 5.1 / Num. unique obs: 3010 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→17.49 Å / SU ML: 0.165 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6584
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2039 2326 5.2 %
Rwork0.1745 42403 -
obs0.176 44729 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 81 534 4179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753741
X-RAY DIFFRACTIONf_angle_d1.04585082
X-RAY DIFFRACTIONf_chiral_restr0.0619524
X-RAY DIFFRACTIONf_plane_restr0.0106680
X-RAY DIFFRACTIONf_dihedral_angle_d16.55611366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.28881490.21942457X-RAY DIFFRACTION97.64
1.94-1.980.22891240.18322452X-RAY DIFFRACTION98.21
1.98-2.030.23511520.18182453X-RAY DIFFRACTION98.3
2.03-2.080.23071470.17152442X-RAY DIFFRACTION98.4
2.08-2.130.2181210.17942477X-RAY DIFFRACTION98.71
2.13-2.20.2051220.17622489X-RAY DIFFRACTION99.05
2.2-2.270.19541280.17442479X-RAY DIFFRACTION99.2
2.27-2.350.19911370.16322531X-RAY DIFFRACTION99.26
2.35-2.440.19071270.17012490X-RAY DIFFRACTION99.47
2.44-2.550.19641490.17712464X-RAY DIFFRACTION99.62
2.55-2.690.22321450.1762492X-RAY DIFFRACTION99.55
2.69-2.850.22631310.18442511X-RAY DIFFRACTION99.77
2.85-3.070.21991550.18712488X-RAY DIFFRACTION99.96
3.07-3.380.21211230.17292569X-RAY DIFFRACTION99.85
3.38-3.870.19141370.15672492X-RAY DIFFRACTION99.7
3.87-4.850.15431420.14972557X-RAY DIFFRACTION99.85
4.85-17.490.18661370.19772560X-RAY DIFFRACTION99.37

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