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- PDB-9oqv: N-hydroxylamine dehydratase (NohD) R144Y/V96A (A1/A2) mutant crys... -

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Basic information

Entry
Database: PDB / ID: 9oqv
TitleN-hydroxylamine dehydratase (NohD) R144Y/V96A (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: 1.88 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)23,3334
Polymers22,5281
Non-polymers8053
Water1,38777
1
A: N-hydroxylamine dehydratase (NohD)
hetero molecules

A: N-hydroxylamine dehydratase (NohD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6668
Polymers45,0572
Non-polymers1,6096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area7600 Å2
ΔGint-126 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.572, 77.572, 88.997
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: 22528.270 Da / Num. of mol.: 1 / Mutation: V96A, 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.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.2M 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: 1.88→38.79 Å / Num. obs: 22732 / % possible obs: 99.8 % / Redundancy: 35.9 % / Biso Wilson estimate: 46.35 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.019 / Net I/σ(I): 26.4
Reflection shellResolution: 1.88→1.92 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1417 / CC1/2: 0.928 / Rpim(I) all: 0.459

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→38.79 Å / SU ML: 0.346 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.5852
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.241 1110 5.03 %
Rwork0.2131 20975 -
obs0.2145 22085 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.54 Å2
Refinement stepCycle: LAST / Resolution: 1.88→38.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 54 77 1607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211596
X-RAY DIFFRACTIONf_angle_d1.21042208
X-RAY DIFFRACTIONf_chiral_restr0.0658241
X-RAY DIFFRACTIONf_plane_restr0.017287
X-RAY DIFFRACTIONf_dihedral_angle_d11.3287232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.970.58761190.57392244X-RAY DIFFRACTION84.91
1.97-2.070.32911400.30882635X-RAY DIFFRACTION99.5
2.07-2.20.33371380.29562645X-RAY DIFFRACTION100
2.2-2.370.36641360.31342502X-RAY DIFFRACTION94.15
2.37-2.610.32441400.25312647X-RAY DIFFRACTION99.43
2.61-2.980.31761420.25282702X-RAY DIFFRACTION100
2.98-3.760.24451440.20852721X-RAY DIFFRACTION99.86
3.76-38.790.18151510.16892879X-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)
14.57074877483-0.638940776828-3.13480606546.61623914877-0.4218691002462.288213293970.282765819463-1.92697024096-0.2042499741461.35744310596-0.502337920658-0.766734138135-0.566627153037-1.415390657280.09226810819261.00865973789-0.0158757808056-0.1484395660391.318152137920.04062767987970.528675481105-8.4478441031617.3743786229-5.40042187638
22.701489995531.24063407778-0.05556064986947.21651056829-1.460319988417.147372714190.028679119817-0.0602776282574-0.4945345134280.509406915598-0.227167944473-0.2229504255840.240775046519-0.08592909800610.502730671810.387429497461-0.0119486519755-0.05513318440330.333583753154-0.06440590164860.431312690422-16.77013444267.55300015758-16.5868096894
36.102881480360.8449641314771.808770594695.490940307371.764520261744.10910676648-0.0380819666493-0.107108981034-0.8890284815540.360988643049-0.0221755858877-0.4768478507930.745379596145-0.142814560160.02466724155580.4951347667940.04718379007230.05703057152870.3249881357370.01053308991860.489370276917-15.84482194090.0107699990366-21.5593672777
47.69124006226-2.1042660827-1.757543541043.31677446976-3.230551982366.14455020883-0.0739122570893-0.3642938069911.770143906790.357068124646-0.334534450847-0.424117244711-0.8083658189850.3914699477910.5285513165980.595288438950.0319507029498-0.1643969839530.497740546216-0.09276286789930.705032641538-10.305439226632.9934329576-14.6748273623
53.587204269810.06809498687440.5048154077012.10350478424-0.006391931461043.286164398340.151904457205-0.182362058947-0.4696640705790.0713110815772-0.156703193493-0.1642873583090.39426745611-0.05585030186170.01654551402690.3811557389740.0652352459954-0.02148295205810.412312014545-0.01946761833490.403640214829-12.9262992788.08391453776-15.6494787826
65.21785023273-0.32581384771-1.204608497492.213846228143.328262628645.06712144512-0.16946814819-0.461515279933-0.413571218712-0.310440373335-0.005578749302422.00066750219-0.0484397255737-0.9123201354310.188283306430.584809179539-0.1478993896960.07151106894310.826476661555-0.2030579165560.828400292412-33.54635845182.47177734627-21.2687125098
72.75246272925-0.1067100740050.2117909471935.576313119721.70225757193.415271095890.0300920328575-0.205461853791-0.4680618105420.233565667893-0.3526467140820.527016149540.586226423178-0.6114283945760.3389694898140.426571679053-0.05084645768730.1341743029020.482064869409-0.03556393032360.435218575083-22.9931970282-0.0645721208181-20.9314961869
87.956584399350.6160633631120.5604045345762.233800409153.55250299776.62355715466-0.300598161395-1.089075594172.127998862740.7097966219410.0941899186392-0.660518371759-1.274643575520.1222218410650.08003052433160.8768004564630.106097252998-0.07305977783770.631082336068-0.2462992701390.884254572817-16.258099849532.1584851798-8.33426578707
93.177947977492.983081999421.025242490013.032842792760.3264782969592.1288687926-0.288518777369-1.61120677025-0.218198028431.00360217254-0.2142945191551.26610216689-0.97897443749-1.38822556450.4119580080180.8983255486270.2194107570580.1174933018640.895956279556-0.1623337556840.781589760905-22.034022769124.6824446928-8.9356711898
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 33 )12 - 3312 - 33
33chain 'A' and (resid 34 through 79 )34 - 7934 - 79
44chain 'A' and (resid 80 through 97 )80 - 9780 - 97
55chain 'A' and (resid 98 through 113 )98 - 11398 - 113
66chain 'A' and (resid 114 through 138 )114 - 138114 - 138
77chain 'A' and (resid 139 through 167 )139 - 167139 - 167
88chain 'A' and (resid 168 through 187 )168 - 187168 - 187
99chain 'A' and (resid 188 through 199 )188 - 199188 - 199

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