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- PDB-9oqw: N-hydroxylamine dehydratase (NohD) H2F/F4P/P5S/R6Y/A59N/R144A (P1... -

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Basic information

Entry
Database: PDB / ID: 9oqw
TitleN-hydroxylamine dehydratase (NohD) H2F/F4P/P5S/R6Y/A59N/R144A (P1/P2/A1) 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: 2 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)46,4045
Polymers45,1092
Non-polymers1,2953
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.898, 86.898, 146.948
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-473-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 10 or (resid 11...
d_2ens_1(chain "B" and (resid 1 through 113 or (resid 114...
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETGLUGLUAA1 - 1141 - 114
d_12ens_1ALAALAHISHISAA116 - 201116 - 201
d_21ens_1METMETGLUGLUBB1 - 1141 - 114
d_22ens_1ALAALAHISHISBB116 - 201116 - 201
d_11ens_2HEMHEMHEMHEMAC301
d_21ens_2HEMHEMHEMHEMBE302

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.127616977247, -0.990258155613, -0.0557018164932), (-0.990984552098, 0.124998297814, 0.0482187001812), (-0.0407863288607, 0.0613531644325, -0.997282439729)-45.6846087475, -37.2848130641, -58.5860185116
2given(-0.11335696829, -0.989707420239, -0.0873465515273), (-0.993293897292, 0.110875722288, 0.0327690068481), (-0.0227471172414, 0.0904753918517, -0.995638876364)-46.5457608666, -38.1096213856, -58.2039669871

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Components

#1: Protein N-hydroxylamine dehydratase (NohD)


Mass: 22554.260 Da / Num. of mol.: 2 / Mutation: H2F, F4P, P5S, R6Y, A59N, R144Y
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: 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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 10,000, 0.2 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: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→38.86 Å / Num. obs: 38860 / % possible obs: 100 % / Redundancy: 51.1 % / Biso Wilson estimate: 43.77 Å2 / CC1/2: 1 / Rpim(I) all: 0.018 / Net I/σ(I): 28.4
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2825 / CC1/2: 0.902 / Rpim(I) all: 0.553

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.86 Å / SU ML: 0.2742 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.8146
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2361 1918 5.17 %
Rwork0.2072 35166 -
obs0.2087 37084 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.64 Å2
Refinement stepCycle: LAST / Resolution: 2→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 90 195 3297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763208
X-RAY DIFFRACTIONf_angle_d1.02744435
X-RAY DIFFRACTIONf_chiral_restr0.0557487
X-RAY DIFFRACTIONf_plane_restr0.0129578
X-RAY DIFFRACTIONf_dihedral_angle_d29.2817455
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.965045355285
ens_2d_2CAX-RAY DIFFRACTIONTorsion NCS0.311854104247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.39661380.34662501X-RAY DIFFRACTION96.67
2.05-2.110.3621350.32622487X-RAY DIFFRACTION96.47
2.11-2.170.3631320.30862356X-RAY DIFFRACTION91.81
2.17-2.240.40211270.3032389X-RAY DIFFRACTION92.16
2.24-2.320.35561380.28822448X-RAY DIFFRACTION95.42
2.32-2.410.31051340.28882463X-RAY DIFFRACTION94.2
2.41-2.520.31881270.27542443X-RAY DIFFRACTION94.55
2.52-2.650.29811320.26812474X-RAY DIFFRACTION94.9
2.65-2.820.31071340.26642420X-RAY DIFFRACTION92.6
2.82-3.040.32691370.25812492X-RAY DIFFRACTION95.01
3.04-3.340.25081410.22192571X-RAY DIFFRACTION97.45
3.34-3.830.21471420.18992597X-RAY DIFFRACTION98.17
3.83-4.820.16161460.1442677X-RAY DIFFRACTION99.33
4.82-38.860.19291550.17132848X-RAY DIFFRACTION99.87
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)
15.847620358573.82622174848-3.002449621926.15822726283-1.966710500864.995920580810.27374943828-0.4475275552330.0003223203323950.202230229187-0.1735827722450.0381905792312-0.1094075585140.334193298834-0.04066764294720.2616243962730.0126974975340.02131660933540.4033974812630.007565649899580.366042063721-21.5371058309-20.0885213523-19.1051637753
24.91602365610.9537554487770.1465064016995.67905944885-1.587423897676.38780934610.1386229513560.2210348360320.997495329130.3462620211260.1321973238850.497665186831-0.72569116212-0.251834132951-0.1858466851160.2978507111170.04615519833380.07420862647880.3609421847440.09640501933520.514161367559-18.4055262697-7.79763263657-25.7656327679
32.388806015721.58030954202-0.8162011350923.84322517081-1.324434086752.353643552280.1116259432780.06363123900390.3102687069440.135260639216-0.1372925417170.0273555464116-0.2050324596540.1832454128170.02334232674120.31671790194-0.01590846856970.0001041852193470.383100128380.07205820443470.303587962834-13.183432062-16.994231742-24.1053114511
49.005233668470.491733186903-3.191940518694.28440264354-3.562579088676.94144017450.0382242102401-0.0873187431131-0.516887788266-0.102838687315-0.28032771518-0.3188567227570.7859485694380.3221038226210.2038561605470.42060012408-0.0044375742434-0.04422097838410.4004955085130.04551475584360.386042858432-18.9055323239-38.851528804-17.8715916757
56.632439757866.68124901885-1.349245637439.23711719986-1.204096810411.92285635295-0.5804000223280.9981830752390.109246543434-1.357557866150.548665558802-0.1166679614820.182123067309-0.119370015116-0.01988584560260.489147774835-0.0165021691148-0.03186232332810.693763423630.1285855767280.396203080556-18.3105229539-20.114254391-44.3989744748
65.899719931532.700288212570.2223268517255.050904505844.053003128814.30229915543-0.164506242380.3315834419470.524723071792-0.2969577275230.1094167673740.836239357421-0.244883320781-0.4188160048350.2147725243830.398024607133-0.00945815236816-0.0198467581160.5719075138860.1766651899370.463220151485-30.7296308481-20.1862918451-30.4093912101
74.481716188452.5879053356-1.869981324111.63141511561-0.25126190167.356040599680.1795767004490.9165412234160.629957116388-0.21103149180.2191935778910.532409736999-0.12931033317-1.25769258457-0.3948283250190.3944257724220.0423963466708-0.06379304014860.7370900313840.2213647411420.524943300263-35.1746634848-20.8543959117-32.9507380057
85.260211853480.6649453557890.1115906544692.13363543837-0.6801750382973.66853577234-0.3162019303940.2977720185840.1148395178170.0939953112690.276717767834-0.105693171105-0.03087832255150.08207889478730.09663564223940.3045627287380.02194182915810.01855449376310.5318825478010.1140895874020.336641420055-11.2454191958-17.4783092999-34.9305630329
95.27134462736-0.16850577895-1.062556760464.347961073180.2425055108676.12844164726-0.1420337706680.996023485011-0.195228473272-0.7081274714390.02274924035750.487441405840.705899347649-0.7687319202880.03325866186750.601954262059-0.290198857457-0.004294168389380.814038711412-0.01396351464360.369468293227-33.5280389223-38.7761271174-35.6388161841
103.422133712690.00396869859177-1.475124538221.0892103488-1.147935182952.68114681257-0.3082654468410.8560735331320.284646375264-0.463465826920.4737743704880.5395078291430.469646094467-0.924748171751-0.1717776513380.503373585048-0.171567820733-0.09454240687390.8622484815020.06986964457570.400113501804-34.556112428-28.9066835303-34.1050763992
115.41687830839-0.7199381508960.5393537673058.13787279883-0.4428978704938.73431140319-0.206821964049-0.711043219717-0.575270137448-0.3110039108940.361823934137-0.7938935414990.005218507584330.606817624053-0.1911339945660.3324826701920.04080755132160.03513270826360.6012993448680.04449076270020.413365409553-0.755800014631-21.8571139979-41.1626675594
124.45366466652-0.1631601070682.227211801838.65445090918-4.032705159912.93473230806-0.458990037760.736045146755-0.208464394346-0.399786996-0.2338382440810.007121525102451.5054227543-0.1198315804790.6912190174720.471370686599-0.02759117030840.09533229262160.6357616968660.004802403700330.576875588819-8.81454691826-27.0666791923-44.2294022404
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 33 )AA1 - 331 - 33
22chain 'A' and (resid 34 through 79 )AA34 - 7934 - 79
33chain 'A' and (resid 80 through 167 )AA80 - 16780 - 167
44chain 'A' and (resid 168 through 201 )AA168 - 201168 - 201
55chain 'B' and (resid 1 through 23 )BC1 - 231 - 23
66chain 'B' and (resid 24 through 45 )BC24 - 4524 - 45
77chain 'B' and (resid 46 through 79 )BC46 - 7946 - 79
88chain 'B' and (resid 80 through 112 )BC80 - 11280 - 112
99chain 'B' and (resid 113 through 138 )BC113 - 138113 - 138
1010chain 'B' and (resid 139 through 167 )BC139 - 167139 - 167
1111chain 'B' and (resid 168 through 187 )BC168 - 187168 - 187
1212chain 'B' and (resid 188 through 201 )BC188 - 201188 - 201

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