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- PDB-9n2a: Crystal structure of N-oxygenase HrmI with the diferrous cofactor... -

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Basic information

Entry
Database: PDB / ID: 9n2a
TitleCrystal structure of N-oxygenase HrmI with the diferrous cofactor and substrate 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 / : / LYSINE / HrmI
Function and homology information
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 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
DepositionJan 28, 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)41,4657
Polymers40,9301
Non-polymers5356
Water4,360242
1
A: HrmI
hetero molecules

A: HrmI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,93014
Polymers81,8602
Non-polymers1,07012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area6510 Å2
ΔGint-84 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.089, 112.089, 67.255
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-574-

HOH

21A-720-

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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2 / 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: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.98 Å3/Da / Density % sol: 58.72 % / Description: hexagonal plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / 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: Sep 5, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.14→17.92 Å / Num. obs: 27105 / % possible obs: 99.76 % / Redundancy: 9.8 % / Biso Wilson estimate: 23.13 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.61
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 3.64 / Num. unique obs: 2666 / CC1/2: 0.874 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→17.92 Å / SU ML: 0.2001 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6085
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2005 1997 7.37 %
Rwork0.1662 25107 -
obs0.1687 27104 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.35 Å2
Refinement stepCycle: LAST / Resolution: 2.14→17.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 30 242 2897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722726
X-RAY DIFFRACTIONf_angle_d0.81983704
X-RAY DIFFRACTIONf_chiral_restr0.046400
X-RAY DIFFRACTIONf_plane_restr0.0085489
X-RAY DIFFRACTIONf_dihedral_angle_d5.6543379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.190.24781420.20721738X-RAY DIFFRACTION100
2.19-2.250.24161440.18541798X-RAY DIFFRACTION100
2.25-2.320.22331380.19381766X-RAY DIFFRACTION100
2.32-2.390.24671440.17921789X-RAY DIFFRACTION100
2.39-2.480.241380.18611756X-RAY DIFFRACTION100
2.48-2.580.23291400.17451788X-RAY DIFFRACTION100
2.58-2.690.20511420.19111802X-RAY DIFFRACTION99.95
2.7-2.840.2431460.17021750X-RAY DIFFRACTION100
2.84-3.010.19791460.17511800X-RAY DIFFRACTION100
3.01-3.240.23261370.17981799X-RAY DIFFRACTION100
3.25-3.570.19231440.16341791X-RAY DIFFRACTION100
3.57-4.080.17891480.14331808X-RAY DIFFRACTION100
4.08-5.120.15671440.13371831X-RAY DIFFRACTION100
5.12-17.920.16931440.16041891X-RAY DIFFRACTION99.9

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