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- PDB-9dq0: Crystal structure of apo HrmJ from Streptomyces sp. CFMR 7 -

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Basic information

Entry
Database: PDB / ID: 9dq0
TitleCrystal structure of apo HrmJ from Streptomyces sp. CFMR 7
ComponentsBsmA domain containing protein
KeywordsOXIDOREDUCTASE / cyclopropanase
Function / homology2OG-Fe dioxygenase / 2OG-Fe dioxygenase / dioxygenase activity / ACETIC ACID / BsmA domain containing protein
Function and homology information
Biological speciesStreptomyces sp. CFMR 7 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZheng, Y.-C. / Chang, W.-C. / Swartz, P.
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

Downloads & links

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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)53,61417
Polymers52,9972
Non-polymers61715
Water9,026501
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.496, 75.033, 86.568
Angle α, β, γ (deg.)90.000, 90.609, 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

#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
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate; 0.1 M sodium cacodylate; pH 6.5; 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.54184 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→17.71 Å / Num. obs: 38520 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 16.13 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.154 / Net I/σ(I): 7.2
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2860 / CC1/2: 0.866

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→17.71 Å / SU ML: 0.2158 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.6137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 1921 4.99 %
Rwork0.1867 36576 -
obs0.1886 38497 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.56 Å2
Refinement stepCycle: LAST / Resolution: 2→17.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3555 0 36 501 4092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083705
X-RAY DIFFRACTIONf_angle_d1.02695045
X-RAY DIFFRACTIONf_chiral_restr0.0625525
X-RAY DIFFRACTIONf_plane_restr0.0109675
X-RAY DIFFRACTIONf_dihedral_angle_d14.65991352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.30511240.22122626X-RAY DIFFRACTION99.82
2.05-2.110.27051240.19642608X-RAY DIFFRACTION100
2.11-2.170.24281320.20082611X-RAY DIFFRACTION100
2.17-2.240.26671300.19722633X-RAY DIFFRACTION99.96
2.24-2.320.29571530.19562563X-RAY DIFFRACTION99.96
2.32-2.410.23941410.20342595X-RAY DIFFRACTION100
2.41-2.520.26691350.20032605X-RAY DIFFRACTION100
2.52-2.650.23481550.19862592X-RAY DIFFRACTION99.96
2.65-2.820.27721320.19762611X-RAY DIFFRACTION99.96
2.82-3.030.20281050.20012652X-RAY DIFFRACTION99.93
3.03-3.340.22951450.18682609X-RAY DIFFRACTION99.82
3.34-3.810.19631610.16842588X-RAY DIFFRACTION99.64
3.82-4.790.18071300.15412626X-RAY DIFFRACTION99.46
4.79-17.710.16831540.17942657X-RAY DIFFRACTION99.36

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