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- PDB-9oqs: N-hydroxylamine dehydratase (NohD) crystal structure with heme -

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Basic information

Entry
Database: PDB / ID: 9oqs
TitleN-hydroxylamine dehydratase (NohD) crystal structure with heme
ComponentsN-hydroxylamine dehydratase (NohD)
KeywordsBIOSYNTHETIC PROTEIN / dehydratase / piperazate synthase / heme / N-N bond / hydroxylamine
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesActinomadura luzonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHiggins, M.A. / Shi, X. / Hoffarth, E.R. / Du, Y.L. / Ryan, K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RPGIN-2021-02626 Canada
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Conversion of a Heme-Dependent Dehydratase to a Piperazate Synthase Reveals the Role of the Heme Propionate Group in N-N Bond-Formation.
Authors: Higgins, M.A. / Mirotadze, N. / Shi, X. / Hoffarth, E.R. / Du, Y.L. / Ryan, K.S.
History
DepositionMay 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-hydroxylamine dehydratase (NohD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2914
Polymers22,5501
Non-polymers7413
Water6,936385
1
A: N-hydroxylamine dehydratase (NohD)
hetero molecules

A: N-hydroxylamine dehydratase (NohD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5828
Polymers45,1012
Non-polymers1,4816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPISA
Unit cell
Length a, b, c (Å)75.714, 75.714, 75.335
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-569-

HOH

21A-710-

HOH

31A-712-

HOH

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Components

#1: Protein N-hydroxylamine dehydratase (NohD)


Mass: 22550.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura luzonensis (bacteria) / Strain: DSM 43766 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 5 % PEG 3350, 0.1 M sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.4→37.86 Å / Num. obs: 43685 / % possible obs: 99.9 % / Redundancy: 25.4 % / Biso Wilson estimate: 14.01 Å2 / CC1/2: 1 / Rpim(I) all: 0.013 / Net I/σ(I): 25.1
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2108 / CC1/2: 0.823 / Rpim(I) all: 0.43

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→33.86 Å / SU ML: 0.1433 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3632 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2066 2019 4.66 %
Rwork0.1864 41314 -
obs0.1873 43333 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.26 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 51 385 1960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771721
X-RAY DIFFRACTIONf_angle_d1.02512383
X-RAY DIFFRACTIONf_chiral_restr0.0929258
X-RAY DIFFRACTIONf_plane_restr0.007318
X-RAY DIFFRACTIONf_dihedral_angle_d16.4235930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.2661410.27592889X-RAY DIFFRACTION99.41
1.44-1.480.27281420.25332910X-RAY DIFFRACTION99.9
1.48-1.520.29681410.23632930X-RAY DIFFRACTION99.97
1.52-1.570.29421440.23612915X-RAY DIFFRACTION99.51
1.57-1.620.26221390.22052904X-RAY DIFFRACTION99.22
1.62-1.690.21941360.20742927X-RAY DIFFRACTION99.93
1.69-1.770.2491390.20262939X-RAY DIFFRACTION99.23
1.77-1.860.21551450.19672924X-RAY DIFFRACTION99.58
1.86-1.970.21541440.20292884X-RAY DIFFRACTION97.65
1.97-2.130.20121460.1782943X-RAY DIFFRACTION99.52
2.13-2.340.20711420.18692945X-RAY DIFFRACTION98.47
2.34-2.680.20471490.18522991X-RAY DIFFRACTION99.68
2.68-3.380.18391470.17093018X-RAY DIFFRACTION99.53
3.38-33.860.17841640.15943195X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.779828908080.960016786839-0.1939682408542.3589256163-0.09690556028221.875855122610.0646353191339-0.2126279070830.01703206501380.194496005144-0.04480518910350.09301178082020.017881577802-0.116875761274-0.03382039502450.07782286341880.01878091444670.02499770679680.120203620985-0.004483166866040.072790298447247.293893107933.919072850628.1491763216
21.474472490350.569949489042-0.3607368044241.3159878053-0.2546210450870.8877007458350.00928087987065-0.04626504880380.07522436737690.06026972491150.08101666269930.176509355001-0.052822139604-0.0488969097215-0.06481004577630.06387904788860.01882137580550.001362393699530.09364922795410.01136076181130.057059626842543.762834642830.496418833121.6974810141
30.9224882341380.258367857126-0.315359724982.24801155578-0.5696973065161.143919436550.0585843979592-0.1811139872350.05056190693410.111603623332-0.105420948686-0.310196573441-0.09448004558880.1991541171730.04523832764330.0969886745468-0.000821512308237-0.01092021682390.134428557603-0.002117335283620.1067444093759.974635254441.221754779125.2737237474
43.57628950496-1.05192218573-1.582834899878.37768063882-0.8494195956455.80786797251-0.0543849630869-0.316525643282-0.8198380326840.184444266134-0.0681822998533-0.02298684945410.4739321509720.2694028136660.1102387104180.1607150238480.016748259764-0.05481347132280.1664680212830.07093337111620.26712751065147.10578628038.4553912643628.4323339949
53.6905220475-0.1956415470065.295266508687.751563541221.13473400117.866317757060.325148703001-0.308074359935-0.06270895643570.813948156738-0.223681067771-0.468557395029-0.0128473603791-0.213550826131-0.003235208420550.20620564888-0.0140886527224-0.04720077982830.1577747904780.03912889669560.1828940961853.66642136316.818299096931.063541379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 167 )
4X-RAY DIFFRACTION4chain 'A' and (resid 168 through 187 )
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 200 )

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