PDB-9pco: Crystal structure of Rv0097 with 5 mM CADA soaked (CADA not bound...

ID or keywords:

Entry

Database: PDB / ID: 9pco

Title

Crystal structure of Rv0097 with 5 mM CADA soaked (CADA not bound) and 5 mM alpha-ketoglutarate soaked (alpha-ketoglutarate bound)

Components

(3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase

Keywords

OXIDOREDUCTASE / non-heme iron enzyme / Fe(II)/alpha-ketoglutarate-dependent dioxygenases / isonitrile synthase

Function / homology

Function and homology information

(R)-3-[(carboxymethyl)amino]fatty acid dioxygenase/decarboxylase / dioxygenase activity / metal ion binding
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.82 Å

Authors

Ye, N. / Drennan, C.L.

Funding support

United States, 2items

Citation

Journal: Nat Commun / Year: 2026
Title: A highly dynamic mononuclear non-heme iron enzyme for the two-step isonitrile biosynthesis.
Authors: Ye, N. / Del Rio Flores, A. / Zhang, W. / Drennan, C.L.

#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...

History

Deposition	Jun 27, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 11, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9pco.cif.gz	582.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9pco.ent.gz	398.5 KB	Display	PDB format
PDBx/mmJSON format	9pco.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pc/9pco ftp://data.pdbj.org/pub/pdb/validation_reports/pc/9pco	HTTPS FTP

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Related structure data

Related structure data	9p9nC 9p9oC 9p9pC 9pasC 9pauC 9paxC 9payC 9pbjC 9pbnC 9pbuC 9pbxC 9pc5C 9pclC 9pcmC 9pcnC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1)

Deposited unit

A: (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase

B: (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase

C: (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase

D: (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase

hetero molecules

138 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase

hetero molecules

C: (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase

hetero molecules

defined by author&software
Evidence: gel filtration
68.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase

D: (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase

hetero molecules

defined by author&software
68.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	88.437, 63.542, 106.594
Angle α, β, γ (deg.)	90.000, 97.887, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	(3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase Mass: 34211.984 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0097, MTCY251.16 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WG83, (R)-3-[(carboxymethyl)amino]fatty acid dioxygenase/decarboxylase

#1: Protein

(3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase

Mass: 34211.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0097, MTCY251.16 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WG83, (R)-3-[(carboxymethyl)amino]fatty acid dioxygenase/decarboxylase

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Non-polymers , 5 types, 865 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-AKG / 2-OXOGLUTARIC ACID Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₆O₅ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 855 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.17 Å³/Da / Density % sol: 43.26 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 270 mM magnesium acetate, 16% w/v PEG 3350

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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: Apr 9, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.82→50 Å / Num. obs: 708866 / % possible obs: 98.5 % / Redundancy: 6.8 % / B_iso Wilson estimate: 27.03 Å² / CC_1/2: 1 / Net I/σ(I): 23.1
Reflection shell	Resolution: 1.82→1.93 Å / Num. unique obs: 115593 / CC_1/2: 0.903

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.82→28.39 Å / SU ML: 0.1987 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2107	5181	5 %
R_work	0.1721	98492	-
obs	0.1741	103673	98.52 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 34.58 Å²

Refinement step

Cycle: LAST / Resolution: 1.82→28.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9140	0	37	855	10032

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	9522
X-RAY DIFFRACTION	f_angle_d	0.8296	12991
X-RAY DIFFRACTION	f_chiral_restr	0.0565	1423
X-RAY DIFFRACTION	f_plane_restr	0.0081	1687
X-RAY DIFFRACTION	f_dihedral_angle_d	12.5314	3571

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 (%)
1.82-1.84	0.3122	171	0.2585	3276	X-RAY DIFFRACTION	98.37
1.84-1.86	0.2662	176	0.2281	3220	X-RAY DIFFRACTION	98.43
1.86-1.89	0.2469	164	0.2148	3315	X-RAY DIFFRACTION	99.06
1.89-1.91	0.264	184	0.2071	3245	X-RAY DIFFRACTION	98.62
1.91-1.93	0.2336	174	0.2015	3268	X-RAY DIFFRACTION	98.85
1.93-1.96	0.2384	170	0.2003	3250	X-RAY DIFFRACTION	98.62
1.96-1.99	0.2621	169	0.2033	3275	X-RAY DIFFRACTION	98.8
1.99-2.02	0.242	163	0.2014	3257	X-RAY DIFFRACTION	98.16
2.02-2.05	0.2377	180	0.1993	3307	X-RAY DIFFRACTION	98.75
2.05-2.08	0.2616	172	0.2098	3220	X-RAY DIFFRACTION	98.23
2.08-2.12	0.2402	176	0.1904	3283	X-RAY DIFFRACTION	98.29
2.12-2.16	0.2338	156	0.1829	3192	X-RAY DIFFRACTION	96.9
2.16-2.2	0.1886	169	0.1745	3186	X-RAY DIFFRACTION	95.94
2.2-2.24	0.2343	177	0.1731	3293	X-RAY DIFFRACTION	99.17
2.24-2.29	0.2076	171	0.1799	3287	X-RAY DIFFRACTION	99.25
2.29-2.35	0.2441	181	0.1826	3318	X-RAY DIFFRACTION	99.21
2.35-2.4	0.244	173	0.1857	3267	X-RAY DIFFRACTION	98.96
2.4-2.47	0.2592	172	0.1857	3315	X-RAY DIFFRACTION	99.03
2.47-2.54	0.2123	169	0.1808	3314	X-RAY DIFFRACTION	99.03
2.54-2.62	0.194	170	0.1801	3266	X-RAY DIFFRACTION	98.82
2.62-2.72	0.2501	180	0.1839	3284	X-RAY DIFFRACTION	98.52
2.72-2.83	0.223	162	0.1956	3193	X-RAY DIFFRACTION	96.33
2.83-2.96	0.2494	178	0.1927	3340	X-RAY DIFFRACTION	99.38
2.96-3.11	0.2443	173	0.1878	3286	X-RAY DIFFRACTION	99.2
3.11-3.31	0.2025	177	0.1783	3332	X-RAY DIFFRACTION	99.21
3.31-3.56	0.2024	173	0.1696	3334	X-RAY DIFFRACTION	99.26
3.56-3.92	0.1982	170	0.1496	3300	X-RAY DIFFRACTION	98.11
3.92-4.48	0.1522	177	0.1341	3281	X-RAY DIFFRACTION	97.46
4.48-5.64	0.1675	179	0.1377	3381	X-RAY DIFFRACTION	99.72
5.64-28.39	0.1898	175	0.1603	3407	X-RAY DIFFRACTION	97.92

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	1.9502901398	0.0102618042688	-0.889990309802	2.17560782043	-0.784380218555	2.66123244096	-0.107033211374	-0.316091889508	0.186060657952	0.108583125866	0.0371968519511	0.0859512278974	-0.0125780122588	0.0577514853753	0.0715265009999	0.171050847404	0.0196578778183	-0.0334827591822	0.221193719668	-0.0634398660017	0.312625619383	-5.2433517695	-12.9662746571	15.1294796961
2	3.16291971303	-0.465486287537	0.430474092206	1.13934302871	0.0659664368424	0.66011295236	-0.219253012414	-0.553457296286	-0.612928537324	0.010031158067	0.157210528933	0.0538664748632	0.10361293155	0.0167426338734	0.0450045717456	0.213001377441	0.0454428207486	0.0463831517505	0.276370526645	0.0724889266157	0.366925422571	9.64232614331	-22.0337449864	5.85969298195
3	1.70182756657	0.379520651595	-0.765897340771	2.10396312776	-0.683157920454	1.94347038126	-0.0399777481202	-0.0717107294445	0.227648762425	-0.126604323582	-0.00544002769959	-0.191560804922	-0.0328071712078	0.233540078801	0.0385292371172	0.176564553585	0.0124668308868	-0.0476811319779	0.199696290962	-0.0237632810553	0.344559792418	1.36220228598	-10.0510298119	4.64273706773
4	2.23678500477	-0.0830529301307	0.269770752653	1.16492519729	-0.450642368803	2.11811859347	-0.0141095377129	0.478002353232	0.0477854058124	-0.337953115912	-0.13594676959	-0.877780152829	-0.186050242979	0.908986233567	0.209717712683	0.356217282316	-0.0870246442159	-0.00121050171317	0.676008853123	0.0586736582138	0.786787984183	9.90427785947	22.6571923511	31.3753108089
5	1.95802801159	0.306321329582	-0.102013368397	2.05635820268	-0.213718870938	2.01293705077	-0.14094218654	0.479459587632	-0.202392283483	-0.219388606924	-0.00751317792565	-0.696265877465	0.106860899363	0.485900334414	0.134569212255	0.26460812829	0.0279708500479	-0.00324937076345	0.393178844385	0.0519998074219	0.491056891523	0.0125058511054	13.0967683245	33.0740411092
6	2.27726580095	0.370880314975	0.940029730482	2.08718125053	0.756498399751	2.97687751909	-0.351281233679	0.505047114127	0.360619542207	-0.618816497967	-0.0691507608642	0.0986166649893	-0.575142623128	-0.169877316341	0.444024622666	0.362827819143	-0.0197070560905	-0.0939493727092	0.312925878469	0.0111887148178	0.372832428822	-15.974579534	16.8071083139	32.8552136076
7	1.63698124684	0.707800619716	-0.735849583098	1.93989967976	0.685704888096	2.20269676063	-0.0316361074138	0.032168151622	0.295329453764	0.199178282726	-0.0970599088183	-0.289367977005	-0.310786410886	0.1824823313	0.110531993355	0.335171659112	0.0032240375029	-0.166440672174	0.227255417418	0.045562618492	0.496055811794	-6.19539006328	21.4239478255	46.1740127517
8	1.78926549222	0.475501615847	1.25668234978	1.11047538507	0.259363410374	3.03322145003	-0.268599256909	-0.358754077762	0.3368685283	0.296012866291	-0.210917405943	-0.201150975423	-0.440643709559	-0.386358922072	0.343908225589	0.368131256981	-0.0324610111114	-0.105879090306	0.302228477205	-0.0445139291046	0.421894086494	-16.8696586695	11.7881404361	50.573387853
9	3.0107232206	0.252985208994	0.710574484174	2.08116597083	0.114343699558	1.84510464852	-0.000226979821127	0.00820611072514	-0.465044317339	0.215610438221	0.22233454622	-0.374789414806	0.0266175949363	0.122978841089	-0.176432937308	0.301389534274	-0.0165372238632	0.00715962691379	0.235130016737	-0.0292298371291	0.316791990993	-26.6943648419	1.9798432021	41.5843924502
10	1.28160859925	0.152217965553	-0.0123243138207	1.9766270725	0.345123279935	1.50749189492	-0.0200085999962	-0.19490900721	0.281455637332	0.538425995912	-0.197599235755	0.0594179511902	-0.190868702566	-0.0910625556602	0.214589181987	0.40612182795	-0.0160861469214	-0.191556045254	0.304092680746	-0.0414452553295	0.481437456566	-10.3552287257	19.3820445968	56.7901823416
11	1.22593719098	0.536731676863	-0.231109043643	1.58309241259	0.91210684153	1.86301251439	-0.162077797606	0.132235410566	0.324415373793	-0.0370936922126	-0.0142857301367	-0.354549907796	-0.237534755895	0.0706189225999	0.159871096873	0.308665499777	-0.013029411035	-0.136720505904	0.306220112631	0.06308812406	0.499644523302	-4.82964898409	19.604508538	39.7843134112
12	1.61527718681	0.433037024643	0.535138268775	2.24540255938	0.770818182789	1.85237377264	0.0320742748007	-0.196789682604	-0.0789788531607	0.128780570736	0.0161347546011	-0.14561837592	0.0501418802677	0.0657123704325	-0.0381116979453	0.14559967317	0.00226907795242	0.0287280480026	0.182594157008	0.0294608537873	0.135202554084	-35.1713803729	31.3935259901	13.6959577641
13	3.44501999193	-1.06896751391	-0.99877883639	1.35359252991	-0.0245599343556	1.77770538213	-0.218868011246	-0.79381272207	0.244542292405	0.152071561379	0.288705931256	0.21856558962	-0.11854779312	0.157244423543	-0.02299612188	0.233243923271	0.045866291757	-0.00191593682484	0.347779801831	-0.0327152339642	0.339415617415	-59.9289063636	42.4381468146	8.65084167165
14	1.6325447317	0.243383668522	0.20245797302	2.03317669389	0.255099023953	1.24937335719	-0.00362910539863	0.0184826860867	-0.0586341020255	-0.115473408836	-0.0214714075745	0.124660793231	0.0337952309961	-0.0540860250327	0.0193424384315	0.16828756255	0.00135138001407	0.0162575838798	0.166948240193	-0.0058310276806	0.151636068045	-44.0879851568	29.7614822269	4.05902262106
15	1.8475812243	-0.0317843549523	-0.721605834679	2.0351623258	0.10327803406	2.10238487087	-0.0112301440365	0.396070727696	-0.000172440873561	-0.170601916674	-0.0353796452076	0.2202552926	0.0402332368614	-0.310592350832	0.0387995429548	0.178115494766	-0.00165269928606	-0.00331787577201	0.231310441953	-0.00364238844273	0.138514797417	-55.162785783	-2.61704275092	36.7464361357
16	0.952430366343	-0.129885678677	-0.0804391969887	0.966583174145	0.0742197835742	0.969522079467	-0.0601698870799	0.00344623474514	0.0258226552722	0.110673858534	0.0413761024961	-0.00796748809045	0.00810635206755	0.013182942329	0.0163918529568	0.223995047376	0.00733855926912	0.0223681908614	0.183406874722	0.00888632539331	0.162450696468	-46.8769676979	-0.140020394575	48.0985422798

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 2 through 147 )	A	A	2 - 147	1 - 146
2	2	chain 'A' and (resid 148 through 195 )	A	A	148 - 195	147 - 194
3	3	chain 'A' and (resid 196 through 290 )	A	A	196 - 290	195 - 285
4	4	chain 'B' and (resid 3 through 26 )	B	C	3 - 26	1 - 24
5	5	chain 'B' and (resid 27 through 78 )	B	C	27 - 78	25 - 76
6	6	chain 'B' and (resid 79 through 97 )	B	C	79 - 97	77 - 95
7	7	chain 'B' and (resid 98 through 144 )	B	C	98 - 144	96 - 142
8	8	chain 'B' and (resid 145 through 160 )	B	C	145 - 160	143 - 158
9	9	chain 'B' and (resid 161 through 178 )	B	C	161 - 178	159 - 176
10	10	chain 'B' and (resid 179 through 239 )	B	C	179 - 239	177 - 237
11	11	chain 'B' and (resid 240 through 290 )	B	C	240 - 290	238 - 286
12	12	chain 'C' and (resid 1 through 144 )	C	E	1 - 144	1 - 137
13	13	chain 'C' and (resid 145 through 178 )	C	E	145 - 178	138 - 171
14	14	chain 'C' and (resid 179 through 290 )	C	E	179 - 290	172 - 283
15	15	chain 'D' and (resid 2 through 144 )	D	G	2 - 144	1 - 143
16	16	chain 'D' and (resid 145 through 290 )	D	G	145 - 290	144 - 289

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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Protein , 1 types, 4 molecules ABCD

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-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 5 types, 865 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

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+Jul 12, 2017. Major update of PDB

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Movie

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Structure viewers

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This web site

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Open data

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 865 molecules

-
Details

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Experimental details

-
Experiment

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Sample preparation

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Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi