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- PDB-9oqz: N-hydroxylamine dehydratase (NohD) A59N/R144Y/V96A (P2/A1/A2) mut... -

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Basic information

Entry
Database: PDB / ID: 9oqz
TitleN-hydroxylamine dehydratase (NohD) A59N/R144Y/V96A (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: 2.13 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,1882
Polymers22,5711
Non-polymers6161
Water57632
1
A: N-hydroxylamine dehydratase (NohD)
hetero molecules

A: N-hydroxylamine dehydratase (NohD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3764
Polymers45,1432
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area6790 Å2
ΔGint-83 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.216, 78.216, 88.560
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: 22571.295 Da / Num. of mol.: 1 / Mutation: 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.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.3M ammonium sulfate

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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: 2.13→39.11 Å / Num. obs: 15977 / % possible obs: 100 % / Redundancy: 28.8 % / Biso Wilson estimate: 73.83 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.019 / Net I/σ(I): 27.3
Reflection shellResolution: 2.13→2.19 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1265 / CC1/2: 0.779 / Rpim(I) all: 0.631

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→39.11 Å / SU ML: 0.4066 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.5722
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2741 797 5.01 %
Rwork0.2259 15124 -
obs0.2284 15921 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.67 Å2
Refinement stepCycle: LAST / Resolution: 2.13→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 43 32 1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831546
X-RAY DIFFRACTIONf_angle_d0.95742144
X-RAY DIFFRACTIONf_chiral_restr0.0563240
X-RAY DIFFRACTIONf_plane_restr0.0141278
X-RAY DIFFRACTIONf_dihedral_angle_d12.3111221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.260.46321280.3942442X-RAY DIFFRACTION99.5
2.26-2.440.41981310.32242468X-RAY DIFFRACTION99.96
2.44-2.680.38161320.34312505X-RAY DIFFRACTION99.96
2.68-3.070.36471310.29952496X-RAY DIFFRACTION100
3.07-3.870.31311330.24382532X-RAY DIFFRACTION100
3.87-39.110.22621420.18792681X-RAY DIFFRACTION99.93
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)
12.66770768602-4.278136589670.06114666265738.07668295710.6860664347520.74521400907-0.0881168112233-2.477088364231.238169741070.9465580422970.272026907707-2.20830589594-0.0666218527573-0.0252869548462-0.3108837836341.2148149627-0.163656313527-0.2495998411691.66235078326-0.135014464050.814814420691-8.839595480616.7778833962-4.65756375866
29.138145460633.175133953042.237765320137.44418581707-1.70775123656.9107278367-0.20396623915-0.323939860018-0.554528937910.230062205286-0.0729189955605-0.3842188725550.610484741060.1892683069410.2477136741290.6056815648150.1259734845570.01269835958240.4722591626960.05111926510940.670211409229-16.8093286986.53635243728-18.5739234549
35.335473175382.292615728771.191966741887.102880295870.4105366593751.80877023215-0.0810798566088-0.0642823668969-0.5553967820640.1327730540590.112321337664-0.6884471602110.3382933124220.360400514516-0.05237963322590.5448827355480.1243338827220.07353839000340.5585272830490.04397112375080.466001011764-13.852403014610.316862549-19.2758355989
46.558987501233.256495957812.246979035347.7612995031.97926732043.650457909110.279028424824-0.610014665462-0.865964314810.466508107649-0.6467138597930.09432892268870.743990714305-0.3844433322790.2806943868090.7537286683840.01557296905160.1344478293610.730365233595-0.007500616418740.593718229425-21.50248730174.11317819795-18.317620338
51.883966295132.739481862712.477856458185.319517991693.827041463293.396837731170.0752427297259-0.933040080669-1.07904984683-1.80590159323-1.963595562853.47538258061-2.10175607567-3.936721049171.882645574311.2721876936-0.04661658183470.2764810773311.35987804477-0.3629535920121.86243226618-38.7859427538.21961276205-22.26140604
65.674657868421.538184226971.142094387889.352540912690.2940020808734.404785774450.08614504552-0.455249813746-0.8481270351790.296214853356-0.3783166873910.4253418770661.15974106045-0.4890264396810.3339131420020.5876781391350.09981635376520.196389099740.5251579870180.003937715860980.534536414928-23.21588387540.553574521896-21.4821814861
72.26879962676-0.243943721168-1.989117398729.566519630150.8904643855045.79853334510.0432089779031-0.5586872516890.9818906523971.56564409760.2872692013890.726692174183-1.0535427072-0.0204802783822-0.5360786137670.9951872473780.166832361417-0.0371842518050.977616467727-0.3272311888580.94847013255-18.912327822529.3010433358-8.17667710773
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 11 )1 - 111 - 11
22chain 'A' and (resid 12 through 45 )12 - 4512 - 45
33chain 'A' and (resid 46 through 97 )46 - 9746 - 97
44chain 'A' and (resid 98 through 128 )98 - 12898 - 128
55chain 'A' and (resid 129 through 138 )129 - 138129 - 138
66chain 'A' and (resid 139 through 167 )139 - 167139 - 167
77chain 'A' and (resid 168 through 199 )168 - 199168 - 199

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