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- PDB-9nh9: Crystal Structure of N-oxygenase HrmI with the diferric cofactor ... -

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Basic information

Entry
Database: PDB / ID: 9nh9
TitleCrystal Structure of N-oxygenase HrmI with the diferric cofactor and the N(6)-hydroxy-L-lysine product bound
ComponentsHrmI
KeywordsOXIDOREDUCTASE / metalloenzyme / oxygenase / diiron
Function / homologyIron-containing redox enzyme / Iron-containing redox enzyme / Pyrroloquinoline-quinone synthase-like / Haem oxygenase-like, multi-helical / oxidoreductase activity / : / : / HrmI
Function and homology information
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSkirboll, S.S. / Phan, H.N. / Swartz, P.D. / Makris, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135315 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: The Heme Oxygenase-Like Diiron Enzyme HrmI Reveals Altered Regulatory Mechanisms for Dioxygen Activation and Substrate N-Oxygenation.
Authors: Skirboll, S.S. / Gangopadhyay, M. / Phan, H.N. / Hartsell, J. / Mudireddy, A. / Hilovsky, D. / Swartz, P.D. / Liu, X. / Guo, Y. / Makris, T.M.
History
DepositionFeb 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HrmI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4807
Polymers40,9301
Non-polymers5506
Water5,386299
1
A: HrmI
hetero molecules

A: HrmI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,96014
Polymers81,8602
Non-polymers1,10012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6350 Å2
ΔGint-87 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.520, 112.520, 67.315
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-568-

HOH

21A-771-

HOH

31A-783-

HOH

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Components

#1: Protein HrmI


Mass: 40929.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8S6W0
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1BX4 / N~6~-hydroxy-L-lysine


Type: L-peptide linking / Mass: 162.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate and HEPES pH 7.5

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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: Mar 22, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.96→17.76 Å / Num. obs: 35485 / % possible obs: 99.62 % / Redundancy: 10.3 % / Biso Wilson estimate: 19.24 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.95
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.79 / Num. unique obs: 3508 / CC1/2: 0.84 / % possible all: 99.91

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→17.5 Å / SU ML: 0.1997 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2363
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2116 2000 5.65 %
Rwork0.1797 33429 -
obs0.1815 35429 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.73 Å2
Refinement stepCycle: LAST / Resolution: 1.96→17.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 0 31 299 2953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822738
X-RAY DIFFRACTIONf_angle_d0.90513723
X-RAY DIFFRACTIONf_chiral_restr0.0512403
X-RAY DIFFRACTIONf_plane_restr0.0077489
X-RAY DIFFRACTIONf_dihedral_angle_d7.0506387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.31371420.23912372X-RAY DIFFRACTION99.96
2.01-2.060.25121450.22782355X-RAY DIFFRACTION99.92
2.06-2.120.25661380.22252376X-RAY DIFFRACTION100
2.12-2.190.24631440.19992381X-RAY DIFFRACTION100
2.19-2.270.2331410.20112346X-RAY DIFFRACTION100
2.27-2.360.2221440.20132355X-RAY DIFFRACTION99.96
2.36-2.470.24471440.19742384X-RAY DIFFRACTION99.92
2.47-2.60.2531390.1942384X-RAY DIFFRACTION99.92
2.6-2.760.24961450.20452366X-RAY DIFFRACTION99.76
2.76-2.970.25031420.18952399X-RAY DIFFRACTION99.22
2.97-3.270.21931430.18332387X-RAY DIFFRACTION99.8
3.27-3.740.19521420.15832419X-RAY DIFFRACTION99.84
3.74-4.690.14641480.1392394X-RAY DIFFRACTION99.41
4.69-17.260.15531430.14842511X-RAY DIFFRACTION99.77

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