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- PDB-9oqt: N-hydroxylamine dehydratase (NohD) T98A/K167A mutant crystal stru... -

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Basic information

Entry
Database: PDB / ID: 9oqt
TitleN-hydroxylamine dehydratase (NohD) T98A/K167A mutant crystal structure with heme and N-hydroxylated ornithine (2.5h soak)
ComponentsN-hydroxylamine dehydratase (NohD)
KeywordsBIOSYNTHETIC PROTEIN / dehydratase / piperazate synthase / heme / N-N bond / hydroxylamine
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / N~5~-hydroxy-L-ornithine
Function and homology information
Biological speciesActinomadura luzonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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)
B: N-hydroxylamine dehydratase (NohD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,74012
Polymers44,9242
Non-polymers1,81610
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-62 kcal/mol
Surface area16790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.703, 67.703, 193.110
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

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Components

#1: Protein N-hydroxylamine dehydratase (NohD)


Mass: 22462.215 Da / Num. of mol.: 2 / Mutation: T98A, K167A
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ONH / N~5~-hydroxy-L-ornithine


Type: L-peptide linking / Mass: 148.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.4 M ammonium phosphate dibasic, 0.2 M sodium chloride, 0.1 M imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.82→64.37 Å / Num. obs: 41379 / % possible obs: 100 % / Redundancy: 19 % / Biso Wilson estimate: 27.29 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.054 / Net I/σ(I): 8.4
Reflection shellResolution: 1.82→1.86 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2394 / CC1/2: 0.836 / Rpim(I) all: 0.415

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→63.89 Å / SU ML: 0.2628 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2142 2065 5.01 %
Rwork0.1912 39148 -
obs0.1924 41213 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.18 Å2
Refinement stepCycle: LAST / Resolution: 1.82→63.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 124 326 3487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713315
X-RAY DIFFRACTIONf_angle_d0.90684569
X-RAY DIFFRACTIONf_chiral_restr0.0579497
X-RAY DIFFRACTIONf_plane_restr0.0096601
X-RAY DIFFRACTIONf_dihedral_angle_d28.9168487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.47051390.42032541X-RAY DIFFRACTION99.78
1.86-1.910.33991310.30812555X-RAY DIFFRACTION99.78
1.91-1.960.30061290.25312573X-RAY DIFFRACTION99.93
1.96-2.020.2511400.21292565X-RAY DIFFRACTION99.82
2.02-2.080.24841310.20862575X-RAY DIFFRACTION99.74
2.08-2.160.26231310.20442566X-RAY DIFFRACTION99.81
2.16-2.240.25651410.20552572X-RAY DIFFRACTION99.85
2.24-2.350.24141390.20932586X-RAY DIFFRACTION99.78
2.35-2.470.30151300.20762596X-RAY DIFFRACTION99.96
2.47-2.620.23991350.21552596X-RAY DIFFRACTION99.67
2.62-2.830.25251390.20482625X-RAY DIFFRACTION99.86
2.83-3.110.23081220.21152635X-RAY DIFFRACTION99.67
3.11-3.560.19971550.17622627X-RAY DIFFRACTION99.57
3.56-4.490.1731470.14382680X-RAY DIFFRACTION99.65
4.49-63.890.14751560.1662856X-RAY DIFFRACTION99.54
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)
16.23993357376-3.17909966744-1.058894039411.641104116730.4181076605721.63538783540.124137946016-0.4760877921550.3690645783460.0407734110710.152606609757-0.120869755216-0.15939463294-0.278134032198-0.2858538807860.407734612-0.04465305599040.003707284719790.509459554479-0.02940785710060.26868032857-3.811706808328.245498734311.999732983
20.857033913333-0.2716356610790.039956034172.821860606541.087544313381.530696942150.00862232551363-0.04715282700550.02355777352520.123443031865-0.03348512492340.06313759224950.0505051551132-0.05965243866580.02535176022280.1791019903650.0123959550435-0.002929518318370.22903495730.02119291728940.162365327318-1.0672521609923.8215804277-3.32384693663
31.8935526585-0.3793777380530.585515855981.371765903351.071668997935.784961384180.1392925232360.0735322972627-0.138265475923-0.012043478574-0.02216286371390.1367938789120.175312978765-0.191926975547-0.1223375106840.193373064197-0.05292906473170.01080019007210.2214438677810.01601432450170.246893849784-8.713196251615.8854545478-14.8193151296
47.65497730801-3.59997354819-3.253252755936.09925734311.403921061283.300737873260.00571672153476-0.8297142192490.3584114989581.026148288980.2845284622481.41126609521-0.578843923287-0.719101031082-0.2022256295740.4552639610230.135824497490.1360699925050.416027092373-0.04561722045490.531226476601-14.494450578641.60969742599.57231000452
57.7838147856-1.01423838025-0.3719520892876.864357344733.996003287053.856256179550.152606079970.6262918631280.1195655530770.3196329511390.003751807134351.94765951961-0.0649857493659-1.10903363769-0.1838371269890.2595074214290.06733557006610.01164613037160.595848209408-0.09690199144790.758692982238-16.560976103434.43887623673.09085558038
60.951661781197-0.103726855191-0.1188054892984.149903028261.726975266993.610992952520.07859349771780.3247630577570.154661250894-0.45745130026-0.175918184854-0.200683623106-0.3599785697720.02033547063120.0953615570650.1669841276120.05218638452590.02509186598110.2943535749060.03091563835320.2576134374486.4971047884634.7569659254-9.26897433308
70.6551494432890.5157399652540.9091019305861.278819429581.481399462573.625558522320.07067294529060.0104154196910.02758243128620.0124591113190.000477755041676-0.0838106516061-0.1335606031330.240180541478-0.0812334827660.222708842213-0.01005976930890.006534613010920.2369615190290.03136979737670.2091276074535.434971145638.4082686854-2.34203227174
87.44300685069-2.40088705674-2.979293517664.281661174281.275260627026.26846304745-0.360045103776-0.005288924196340.534048102992-0.02641238634580.279780535594-0.144669781621-0.4003682100220.1545736611190.09157843752920.3526984821420.0279798433143-0.09524721257550.295022087410.02015493118270.301662784325-7.6183564154837.145755165-24.5915757277
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 11 )AA1 - 111 - 11
22chain 'A' and (resid 12 through 113 )AA12 - 11312 - 113
33chain 'A' and (resid 114 through 167 )AA114 - 167114 - 167
44chain 'A' and (resid 168 through 185 )AA168 - 185168 - 185
55chain 'A' and (resid 186 through 202 )AA186 - 202186 - 202
66chain 'B' and (resid 1 through 45 )BD1 - 451 - 45
77chain 'B' and (resid 46 through 167 )BD46 - 16746 - 167
88chain 'B' and (resid 168 through 206 )BD168 - 206168 - 206

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