PDB-9oqu: N-hydroxylamine dehydratase (NohD) T98A/K167A mutant crystal stru...

ID or keywords:

Entry

Database: PDB / ID: 9oqu

Title

N-hydroxylamine dehydratase (NohD) T98A/K167A mutant crystal structure with heme and N-hydroxylated ornithine (5h soak)

Components

N-hydroxylamine dehydratase (NohD)

Keywords

BIOSYNTHETIC PROTEIN / dehydratase / piperazate synthase / heme / N-N bond / hydroxylamine

Function / homology

PROTOPORPHYRIN IX CONTAINING FE / N~5~-hydroxy-L-ornithine

Function and homology information

Biological species

Actinomadura luzonensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

Higgins, M.A. / Shi, X. / Hoffarth, E.R. / Du, Y.L. / Ryan, K.S.

Funding support

Canada, 1items

Citation

Journal: 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

Deposition	May 21, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9oqu.cif.gz	215.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9oqu.ent.gz	143.5 KB	Display	PDB format
PDBx/mmJSON format	9oqu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9oqu_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	9oqu_full_validation.pdf.gz	1.4 MB	Display
Data in XML	9oqu_validation.xml.gz	25 KB	Display
Data in CIF	9oqu_validation.cif.gz	33.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oq/9oqu ftp://data.pdbj.org/pub/pdb/validation_reports/oq/9oqu	HTTPS FTP

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Related structure data

Related structure data	9oqsC 9oqtC 9oqvC 9oqwC 9oqxC 9oqzC 9or0C 9or1C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: N-hydroxylamine dehydratase (NohD)

B: N-hydroxylamine dehydratase (NohD)

hetero molecules

46.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	67.813, 67.813, 193.619
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2
Space group name Hall	P4abw2nw
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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	PRO	PRO	(chain 'A' and (resid 1 through 10 or (resid 11...	A	A	1 - 72	1 - 72
1	2	LEU	LEU	THR	THR	(chain 'A' and (resid 1 through 10 or (resid 11...	A	A	75 - 107	75 - 107
1	3	VAL	VAL	GLU	GLU	(chain 'A' and (resid 1 through 10 or (resid 11...	A	A	110 - 200	110 - 200
2	1	MET	MET	PRO	PRO	(chain 'B' and (resid 1 through 16 or (resid 17...	B	B	1 - 72	1 - 72
2	2	LEU	LEU	THR	THR	(chain 'B' and (resid 1 through 16 or (resid 17...	B	B	75 - 107	75 - 107
2	3	VAL	VAL	GLU	GLU	(chain 'B' and (resid 1 through 16 or (resid 17...	B	B	110 - 200	110 - 200

#1: Protein	N-hydroxylamine dehydratase (NohD) Mass: 22462.215 Da / Num. of mol.: 2 / Mutation: T98A, K167A 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-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
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.35 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 1.4 M ammonium phosphate dibasic, 0.2 M sodium chloride, 0.1 M imidazole pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.73→38.49 Å / Num. obs: 47538 / % possible obs: 98.8 % / Redundancy: 51.7 % / B_iso Wilson estimate: 30.72 Å² / CC_1/2: 1 / R_pim(I) all: 0.021 / Net I/σ(I): 20.5
Reflection shell	Resolution: 1.73→1.76 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2629 / CC_1/2: 0.937 / R_pim(I) all: 0.507

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.73→38.49 Å / SU ML: 0.211 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3603 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2329	1984	4.21 %
R_work	0.1883	45121	-
obs	0.1901	47105	97.73 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 43.66 Å²

Refinement step

Cycle: LAST / Resolution: 1.73→38.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3053	0	96	328	3477

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	3270
X-RAY DIFFRACTION	f_angle_d	1.0138	4518
X-RAY DIFFRACTION	f_chiral_restr	0.0543	493
X-RAY DIFFRACTION	f_plane_restr	0.0113	592
X-RAY DIFFRACTION	f_dihedral_angle_d	11.3371	2538

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.73-1.77	0.3559	139	0.3083	3168	X-RAY DIFFRACTION	97.7
1.77-1.82	0.3278	138	0.2853	3123	X-RAY DIFFRACTION	97.37
1.82-1.87	0.2921	132	0.2564	3020	X-RAY DIFFRACTION	93.14
1.87-1.94	0.2853	140	0.2445	3157	X-RAY DIFFRACTION	96.91
1.94-2	0.3011	140	0.2411	3187	X-RAY DIFFRACTION	98.34
2-2.08	0.2654	140	0.2201	3178	X-RAY DIFFRACTION	97.93
2.08-2.18	0.3045	143	0.2222	3235	X-RAY DIFFRACTION	98.54
2.18-2.29	0.2813	140	0.2183	3192	X-RAY DIFFRACTION	98.32
2.29-2.44	0.3034	136	0.2309	3121	X-RAY DIFFRACTION	94.98
2.44-2.63	0.2407	145	0.2201	3262	X-RAY DIFFRACTION	99.16
2.63-2.89	0.2681	145	0.2156	3294	X-RAY DIFFRACTION	99.48
2.89-3.31	0.2701	145	0.1961	3315	X-RAY DIFFRACTION	99.51
3.31-4.17	0.1953	146	0.1514	3332	X-RAY DIFFRACTION	98.11
4.17-38.49	0.1754	155	0.1496	3537	X-RAY DIFFRACTION	98.53

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	9.87755268654	0.734792688857	-3.77710829105	4.96147262553	-3.66263099722	6.35710285786	-0.135199138268	0.139743243199	0.224830432001	0.252864196725	0.577222457434	0.13436197091	-0.0594677473767	-0.703686743874	-0.327847360252	0.489017382065	0.0564471373501	-0.00297551293386	0.556769247299	0.0202005219102	0.288998162663	-5.16634918156	27.7094482678	12.0111095825
2	6.00224162819	1.96109395494	-2.96070167035	1.99419736357	-0.114275589324	2.03733718919	0.213252099239	-0.136947918307	-0.0580162057703	0.490683468759	-0.0957658334272	0.69274132024	0.073428881994	-0.547353069188	-0.224328173499	0.33834497081	0.0270692576042	0.0637428491897	0.429086946156	0.0360073875796	0.415215075883	-12.1572459677	21.4198619999	1.41748863629
3	7.91058264308	2.75080075543	0.252649375364	2.63898009635	-0.614489782079	3.39877412077	-0.252540447889	0.122718511667	-0.220376361593	-0.0614642847756	0.221323117827	-0.0464178308164	0.154695351233	0.112299612384	0.0394332722006	0.237497937499	0.0540825292404	-0.0124835350657	0.236595009552	-0.00352743979651	0.206728034025	2.22881988189	21.5811320647	-8.01091386075
4	2.85986150417	-0.8799109643	-0.556142284602	3.99993984919	0.617041484908	5.45839039254	-0.070254791782	-0.0239794204237	-0.108383490515	0.228975663108	0.0781293395389	-0.0212084921508	0.414170599902	0.156033449071	0.0394072097532	0.23125596675	0.0416489157047	-0.037518889321	0.251043228294	-0.00881753266724	0.218091921762	2.20770477806	15.8787469859	-8.33466438274
5	5.06091276316	-0.31740791874	0.93495382058	2.6760628053	-2.31659536885	2.76749170363	-0.22668266459	-0.276497543991	0.724659909694	0.293893754643	-0.135824874354	0.296885259982	-0.940115517788	-0.435855517571	0.430647079209	0.396071178538	0.0997009105514	0.00869839074561	0.341040834753	-0.057141508858	0.397697663118	-6.49249243628	46.1323481843	7.5345824184
6	0.857262455706	-0.447230812971	-0.36409344618	3.97230144468	1.07039848588	3.14095780664	-0.114370156388	-0.091416004483	-0.154267375281	0.356729922976	0.153290107106	0.246221082322	0.334726753979	0.114131919078	-0.017786019935	0.235380108541	0.0771066807089	-0.0134814284469	0.327087598486	0.0123369251969	0.237550636424	-0.0106166138953	21.5226143166	-0.864303768177
7	5.6897868541	-1.42582166399	0.786636545037	3.29399400182	0.180342626482	7.26719433388	0.171961556127	0.00745361620363	-0.226470301391	0.0425275847799	0.120338321007	0.416451468125	-0.00223439192934	-0.454098679328	-0.302897884193	0.231074342783	-0.0529096057204	-0.000303869348788	0.341750831085	0.0213139383283	0.31817087865	-13.931557087	16.26259055	-17.2754878743
8	1.87912304124	-0.730615267597	-0.350779017878	2.37934882005	1.62636589603	5.70618249669	-0.00336299088965	0.0630559992578	-0.20279906917	0.159442150748	0.0722765491746	0.0743363823498	0.731710974194	0.266104802975	-0.0830942652112	0.214565185018	-0.0465688641196	0.00115189557464	0.275109384061	0.0284820674783	0.315219014032	-4.37451917572	15.3807541986	-12.2980380486
9	6.79826727575	-0.575062774358	0.28885001267	8.86824155389	-0.525446839615	2.76460061866	0.305606049946	-0.31272719713	1.01478111827	1.010518404	-0.137939202401	1.17403009488	-0.65689918976	-0.578060132339	-0.0884780075359	0.530643811551	0.179539520878	0.215091926529	0.49739929834	0.0292246792298	0.685146069582	-14.6237893283	41.9508848316	8.85371648164
10	5.35421273067	0.917200353678	0.420264371259	3.147779791	-1.95101368799	2.93397420698	-0.0316815149167	-0.0355687660044	-0.388118686599	0.532984839178	0.253826177307	1.48673153179	-0.150668704568	-1.92376756786	-0.285095081358	0.376459270689	0.0876419781871	0.0601990575737	0.768513684513	-0.0182091049525	0.676512783048	-16.9228307038	33.0966701059	4.18721379619
11	8.78908814861	-0.58164134735	3.42149917359	5.79214607867	4.112300648	5.17867971515	0.399351542373	-0.427947517281	0.643159753938	-1.1012166896	-0.478712256754	-0.0963124881047	0.35133478125	0.364662909841	0.0951200509815	0.872296654564	0.109395361844	0.216969470752	0.709509268938	0.0928131876178	0.502864293229	5.38351073321	30.7020813197	-22.1175471478
12	9.22677213913	0.455376350185	-5.72882485452	1.96763832354	-0.0640155197102	3.66531327967	0.349919034085	0.850697009925	0.746052718091	-0.616740864597	-0.000847562308124	-0.250066090226	-1.32930926995	-0.450886779029	-0.424494817352	0.491838951605	0.0765435993518	-0.00518559123162	0.359989066172	0.0582911565044	0.328911175827	5.23469605069	43.3003031084	-13.2879992517
13	0.902783806201	-0.771015586674	-0.4039060743	2.29450639487	-1.70660893196	3.94816289253	0.234511658086	0.076303044607	-0.0166125805245	-0.0372951468932	-0.257260101262	-0.264710868137	0.0586971860312	0.317294647718	0.0275249441638	0.174001345303	0.0506706130036	-0.0356204926243	0.249886253148	-0.0257912436068	0.233066736478	7.54008058045	32.104439512	-0.390016528554
14	1.51932233347	0.294635060427	1.11636893124	1.39139552081	1.16281401075	4.18519894326	0.0106246277391	0.00594986488609	0.0931369937603	0.048822504494	0.0622351527748	-0.0351930308513	-0.156662924197	0.211752825075	-0.0965501560137	0.222366141043	0.0276312424717	0.0145292905506	0.262889335759	0.0552991590303	0.239215608503	4.38476582646	37.0241186354	-4.01394010024
15	1.86252366308	-0.416045423284	0.544836730366	1.94830875529	2.19848774918	6.56742909374	-0.00765269978531	-0.0232903593162	0.133006794614	0.158180143906	0.150060822103	-0.140589698298	0.0312377787946	0.443665998663	-0.165099731645	0.296278056307	-0.0583525855697	0.023364762374	0.241332537926	0.0394919530515	0.252751583198	8.67355828973	42.0917019723	3.70052003144
16	4.09718273543	-0.769661107817	-0.270375089127	4.42753067952	-3.19199456317	5.34904666015	-0.164616684193	0.399798880983	-0.0467984821952	-0.230831596489	0.0613004812893	0.356423298297	-0.205969178896	-0.308947272528	0.0432355290326	0.332008393557	0.0434438948896	-0.0731805857256	0.425319375465	0.00331894350844	0.308575517897	-10.8392182183	34.7024086907	-26.1672925335
17	1.16491271957	-2.49651813949	-1.06089753178	6.18520570542	4.10421915717	4.340683188	0.276010765861	0.359257902001	0.896079912719	-0.134845802512	0.349284373199	-0.449267569933	-0.692831622048	0.1577723305	-0.600337150518	0.405203764021	0.0603557894695	-0.125001311079	0.474897129781	0.0318985631645	0.423719378785	-3.55812225861	40.2168801215	-22.97937667

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 21 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 22 through 45 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 46 through 79 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 80 through 97 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 98 through 113 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 114 through 138 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 139 through 167 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 168 through 187 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 188 through 201 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 11 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 12 through 21 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 22 through 45 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 46 through 138 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 139 through 167 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 168 through 185 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 186 through 206 )

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