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- PDB-9dq2: Crystal structure of HrmJ from Streptomyces sp. CFMR 7 (HrmJ-ssc)... -

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Basic information

Entry
Database: PDB / ID: 9dq2
TitleCrystal structure of HrmJ from Streptomyces sp. CFMR 7 (HrmJ-ssc) complexed with vanadyl(IV)-oxo, succinate and 6-nitronorleucine
ComponentsBsmA domain containing protein
KeywordsOXIDOREDUCTASE / cyclopropanase
Function / homology2OG-Fe dioxygenase / 2OG-Fe dioxygenase / dioxygenase activity / 6-nitro-L-norleucine / BROMIDE ION / SUCCINIC ACID / oxovanadium(2+) / BsmA domain containing protein
Function and homology information
Biological speciesStreptomyces sp. CFMR 7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 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)54,49917
Polymers52,9972
Non-polymers1,50215
Water11,872659
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.113, 78.836, 97.166
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 , 6 types, 674 molecules

#2: Chemical ChemComp-6HN / 6-nitro-L-norleucine


Type: L-peptide linking / Mass: 176.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12N2O4 / 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: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaBr; 20% (w/v) PEG 3350

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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: 1.55→50 Å / Num. obs: 84079 / % possible obs: 99.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 12.73 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.172 / Rsym value: 0.172 / Net I/σ(I): 10.8
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 4147 / CC1/2: 0.976

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→41.36 Å / SU ML: 0.1698 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.2236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 4007 4.91 %
Rwork0.1957 77619 -
obs0.1965 81626 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.46 Å2
Refinement stepCycle: LAST / Resolution: 1.55→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 78 659 4301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00993855
X-RAY DIFFRACTIONf_angle_d1.20875254
X-RAY DIFFRACTIONf_chiral_restr0.0754546
X-RAY DIFFRACTIONf_plane_restr0.0138702
X-RAY DIFFRACTIONf_dihedral_angle_d13.82271429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.3281400.30392285X-RAY DIFFRACTION83.77
1.57-1.590.26241370.25352527X-RAY DIFFRACTION93.51
1.59-1.610.29641260.25082599X-RAY DIFFRACTION95.51
1.61-1.630.28741360.23312681X-RAY DIFFRACTION97.14
1.63-1.650.25021370.21942662X-RAY DIFFRACTION97.83
1.65-1.670.24121480.21022689X-RAY DIFFRACTION98.13
1.67-1.70.22671430.2042682X-RAY DIFFRACTION98.64
1.7-1.730.20611130.19582692X-RAY DIFFRACTION98.18
1.73-1.750.22491420.19922721X-RAY DIFFRACTION98.28
1.75-1.780.23251130.19452693X-RAY DIFFRACTION97.97
1.78-1.820.21991250.20282657X-RAY DIFFRACTION97.51
1.82-1.850.22561580.21212673X-RAY DIFFRACTION97.86
1.85-1.890.23691480.21252675X-RAY DIFFRACTION97.99
1.89-1.930.20571790.21292617X-RAY DIFFRACTION97.02
1.93-1.980.21711320.18342676X-RAY DIFFRACTION96.53
1.98-2.030.20221450.18782657X-RAY DIFFRACTION96.85
2.03-2.080.1861650.18382646X-RAY DIFFRACTION96.9
2.08-2.140.20791560.18062649X-RAY DIFFRACTION97.63
2.14-2.210.22261420.18852688X-RAY DIFFRACTION97.45
2.21-2.290.21481210.18182691X-RAY DIFFRACTION97.54
2.29-2.380.19271220.1812708X-RAY DIFFRACTION97.38
2.38-2.490.22261370.19982693X-RAY DIFFRACTION96.98
2.49-2.620.26031310.2012703X-RAY DIFFRACTION96.72
2.62-2.780.20661020.20022745X-RAY DIFFRACTION97.27
2.78-30.241300.19222743X-RAY DIFFRACTION98.32
3-3.30.19391380.1932753X-RAY DIFFRACTION97.73
3.3-3.780.18431370.17822741X-RAY DIFFRACTION97.23
3.78-4.760.1611530.1722759X-RAY DIFFRACTION97.39
4.76-41.360.19891510.21072914X-RAY DIFFRACTION97.61

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