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- PDB-9or0: N-hydroxylamine dehydratase (NohD) H2F/F4P/P5S/R6Y/A59N/R144Y/V96... -

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Basic information

Entry
Database: PDB / ID: 9or0
TitleN-hydroxylamine dehydratase (NohD) H2F/F4P/P5S/R6Y/A59N/R144Y/V96A (P1/P2/A1/A2) mutant 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: 1.75 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)46,4106
Polymers45,0522
Non-polymers1,3574
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-71 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.101, 87.101, 147.377
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
11B-545-

HOH

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Components

#1: Protein N-hydroxylamine dehydratase (NohD)


Mass: 22526.207 Da / Num. of mol.: 2 / Mutation: H2F, F4P, P5S, R6Y, A59N, R144Y, V96A
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.: 2 / Source method: obtained synthetically / 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.: 352 / 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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 14% PEG 8000, 0.1 M ammonium acetate, 0.1 M Bis-Tris pH 5.5

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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: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→38.95 Å / Num. obs: 57903 / % possible obs: 99.9 % / Redundancy: 28.6 % / Biso Wilson estimate: 36.76 Å2 / CC1/2: 1 / Rpim(I) all: 0.012 / Net I/σ(I): 39
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3116 / CC1/2: 0.68 / Rpim(I) all: 0.845

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→38.95 Å / SU ML: 0.2808 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.2092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2213 1989 3.46 %
Rwork0.1942 55555 -
obs0.1952 57544 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.68 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 94 352 3494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743309
X-RAY DIFFRACTIONf_angle_d1.13934574
X-RAY DIFFRACTIONf_chiral_restr0.0607493
X-RAY DIFFRACTIONf_plane_restr0.0138605
X-RAY DIFFRACTIONf_dihedral_angle_d11.0108478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.46041390.41843860X-RAY DIFFRACTION98.23
1.79-1.840.38131410.32413921X-RAY DIFFRACTION99.75
1.84-1.90.37411400.2923917X-RAY DIFFRACTION99.8
1.9-1.960.3331400.27913915X-RAY DIFFRACTION99.7
1.96-2.030.2981410.24323933X-RAY DIFFRACTION99.51
2.03-2.110.24151420.23283902X-RAY DIFFRACTION99.36
2.11-2.20.28741410.22673945X-RAY DIFFRACTION99.73
2.2-2.320.2781400.23453923X-RAY DIFFRACTION98.9
2.32-2.470.24921410.21563955X-RAY DIFFRACTION99.32
2.47-2.660.24351410.20623952X-RAY DIFFRACTION98.98
2.66-2.920.22571420.20543974X-RAY DIFFRACTION99.42
2.92-3.350.23231430.19674012X-RAY DIFFRACTION99.12
3.35-4.220.18251450.16984065X-RAY DIFFRACTION99.69
4.22-38.950.18161530.15974281X-RAY DIFFRACTION99.62
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)
15.352505458382.88064742139-2.132645805893.909524035120.4859232438942.150260129130.481423343436-0.400386342190.09871296184140.337885007338-0.2736782233340.138122026128-0.1287754238380.130297425225-0.1076135075850.192291644145-0.006190083786550.009500212334010.3388092546830.0436839587990.27625421544-21.2636106625-20.126843493-19.1067381532
22.684320645691.57015382815-1.229661977713.17251203874-1.463765392762.19413542160.248253155691-0.01585893495290.4756450494610.203433681134-0.1169975425420.18536328206-0.2883841633040.059223265059-0.1206813047760.2141043195810.004932414152130.01919849031330.2807171244120.03034097065010.260579162033-14.8184148943-13.8543599187-24.7159994596
35.159601960652.06585567134-2.78731224152.48351556189-4.045856418858.16156864528-0.039946934526-0.0366449799185-0.322104966109-0.190511316308-0.208760356869-0.6423255600450.5586604306760.5489399129360.1755185465270.3586322712530.0273367082752-0.02011767818230.3344225853890.03008777545350.370950876079-19.0671477117-39.3632782828-17.9465056712
44.414311097262.72236725128-0.08186708318824.51466927625-2.181995409131.74555053957-0.3202103151260.8680672500950.275751261483-0.6748898066220.507975126330.1151294414220.275174879843-0.461536549277-0.1170830890970.314284506156-0.0383080805681-0.03677299532270.5089638063690.1209148250630.291227714825-21.7294097252-19.5569445281-40.5311851616
52.002666447331.49290427525-0.2636742892431.56554561559-0.5058420865053.610450853270.01768600758160.7933405268710.515865202541-0.152667558140.3395594228330.488119109353-0.083651813607-1.03175953266-0.2993065783010.271484101861-0.0335353776356-0.05488462529730.6567786523860.1977388890380.434209885421-34.2772187471-21.1394567488-32.8610406013
61.294345571620.710003877630.4206527833585.65475279728-0.3511099285985.49287372888-0.151273156077-0.0890724625727-0.07407616457440.2070119238370.0871713153946-0.487872160967-0.07651795832320.4275036575790.04241378074230.2016164630090.000190947587505-0.02190693060230.3791778276680.06421528649160.286555500574-0.290216383653-17.2039922625-33.6560667737
74.23929525810.267848892518-0.864615711971.294228928620.4925503371910.7038951251380.3227190313240.4089753366880.152698540161-0.1653569804710.1244998426740.334508483006-0.205065639935-0.838877568486-0.3424747787870.23352271247-0.00301080021955-0.005622797191030.6997053451710.2269347880480.384960986588-24.5280457949-17.759801807-36.7637455502
83.6503827882-0.3084688929090.3739978285054.20675711881-1.403599656193.67237035092-0.438862635560.943960897323-0.419282193681-0.4804248551530.2411983050060.2615458916780.786091657487-0.5891221542080.1245907938070.508898729557-0.264990117092-0.02390877585650.700954594926-0.02597613270350.270303403848-33.1854451542-39.0423576292-35.8044733375
91.59496089349-0.586052420275-0.7760478697450.2235536882080.3406813415961.16838639877-0.2829646897460.88661917350.324205031381-0.3202086424110.4114316034530.5331542358970.449919939751-0.956716693693-0.08049734543970.38727206285-0.168903395663-0.09404389764680.7668652072920.0957572367750.377052321273-34.2885561303-28.2700223855-34.6033572015
108.822249758660.882679580778-2.187823257125.85061959308-0.944206647628.38367994408-0.154249835389-0.616589596208-0.356919936761-0.1298413897360.341072499781-0.608055635780.4888150402161.01120649601-0.1233781741190.2741787020430.06109366973870.03749717000160.4972488727760.006474217845790.350735950769-0.500404726383-22.0113902765-41.2839382771
118.334174468571.01564974666-1.435164544112.92620765216-2.905929691482.93696780449-0.239752764611.09110813352-0.436231783993-0.874685863213-0.2087842686120.05671421810281.78618581175-0.6760617426090.3975815271890.543265850306-0.06234017772320.05230812583220.540142925736-0.02068584180460.422388408446-9.32756003262-27.3822437019-45.3782284158
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 34 )AA1 - 341 - 34
22chain 'A' and (resid 35 through 167 )AA35 - 16735 - 167
33chain 'A' and (resid 168 through 201 )AA168 - 201168 - 201
44chain 'B' and (resid 1 through 33 )BD1 - 331 - 33
55chain 'B' and (resid 34 through 79 )BD34 - 7934 - 79
66chain 'B' and (resid 80 through 97 )BD80 - 9780 - 97
77chain 'B' and (resid 98 through 112 )BD98 - 11298 - 112
88chain 'B' and (resid 113 through 138 )BD113 - 138113 - 138
99chain 'B' and (resid 139 through 167 )BD139 - 167139 - 167
1010chain 'B' and (resid 168 through 187 )BD168 - 187168 - 187
1111chain 'B' and (resid 188 through 203 )BD188 - 203188 - 203

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