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- PDB-9or1: N-hydroxylamine dehydratase (NohD) H2F/F4P/P5S/R6Y/A59N/R144Y/V96... -

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Basic information

Entry
Database: PDB / ID: 9or1
TitleN-hydroxylamine dehydratase (NohD) H2F/F4P/P5S/R6Y/A59N/R144Y/V96A/D172E/L172Q/D173P/R176V (P1/P2/A1/A2/A3) mutant crystal structure with heme and N-hydroxylated ornithine
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: 1.5 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)23,4534
Polymers22,4791
Non-polymers9743
Water4,666259
1
A: N-hydroxylamine dehydratase (NohD)
hetero molecules

A: N-hydroxylamine dehydratase (NohD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9068
Polymers44,9582
Non-polymers1,9486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7350 Å2
ΔGint-86 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.904, 101.904, 51.812
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-625-

HOH

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Components

#1: Protein N-hydroxylamine dehydratase (NohD)


Mass: 22479.168 Da / Num. of mol.: 1
Mutation: H2F, F4P, P5S, R6Y, A59N, R144Y, V96A, D171E, L172Q, D173P, R176V
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-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#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.: 259 / 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

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 16% PEG 3350, 0.1 M Bis-Tris pH 6.5

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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: Mar 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.5→36.33 Å / Num. obs: 49786 / % possible obs: 100 % / Redundancy: 39.4 % / Biso Wilson estimate: 22.99 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.029 / Net I/σ(I): 14.9
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2452 / CC1/2: 0.737 / Rpim(I) all: 0.879

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→36.329 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1779 2003 4.03 %
Rwork0.1627 --
obs0.1633 49658 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→36.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 67 259 1845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071710
X-RAY DIFFRACTIONf_angle_d0.8642363
X-RAY DIFFRACTIONf_dihedral_angle_d11.0841320
X-RAY DIFFRACTIONf_chiral_restr0.053250
X-RAY DIFFRACTIONf_plane_restr0.005312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.53780.30131410.28523301X-RAY DIFFRACTION98
1.5378-1.57930.32991420.26073352X-RAY DIFFRACTION100
1.5793-1.62580.27871370.22863388X-RAY DIFFRACTION100
1.6258-1.67830.22361450.2083381X-RAY DIFFRACTION100
1.6783-1.73830.21321370.19423386X-RAY DIFFRACTION100
1.7383-1.80790.18211430.19323375X-RAY DIFFRACTION100
1.8079-1.89010.20451420.18013398X-RAY DIFFRACTION100
1.8901-1.98980.21571430.19123406X-RAY DIFFRACTION100
1.9898-2.11440.18711420.17223388X-RAY DIFFRACTION100
2.1144-2.27770.18691380.16623414X-RAY DIFFRACTION100
2.2777-2.50680.17471450.17083425X-RAY DIFFRACTION100
2.5068-2.86950.17971420.17213436X-RAY DIFFRACTION100
2.8695-3.61470.16911490.15033446X-RAY DIFFRACTION100
3.6147-36.30.14371570.12963559X-RAY DIFFRACTION100
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)
12.60560.24620.19595.2165-1.2325.5137-0.4764-0.8722-0.19840.54040.28330.3598-0.2309-0.16610.09250.26940.1270.0340.3460.05480.278633.07530.977611.6248
24.05350.03810.44156.17690.15926.0234-0.3408-0.5011-0.29830.35810.14220.16610.06690.30310.09570.14070.11240.08970.26110.03780.16519.560538.42259.6688
32.9419-1.4187-0.19610.82140.2185-0.0377-0.1533-0.2439-0.38070.11110.08780.22180.0288-0.01970.0560.21210.02810.03530.24740.02980.210417.104940.32626.6508
42.6308-0.7887-0.52730.93390.27750.3402-0.1819-0.3218-0.60870.15990.10190.37140.0890.06170.05970.21410.03770.05310.24360.03720.23339.664142.45269.502
52.18870.9242-1.93575.06911.14546.66090.0773-0.29710.50070.11470.09930.0965-0.69980.0909-0.1610.24970.01310.00150.1939-0.01410.242644.230443.4046.3149
62.7009-0.37221.8728.5035-4.35019.3347-0.0588-1.54520.72691.225-0.02760.5909-0.4246-0.4770.00530.44040.03010.06230.5525-0.13780.374936.044245.428812.2286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 33 )
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 138 )
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 167 )
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 187 )
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 201 )

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