PDB-9zav: Crystal structure of Formyl-coenzyme A transferase from Brucella ...

ID or keywords:

Entry

Database: PDB / ID: 9zav

Title

Crystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with succinate

Components

Formyl-coenzyme a transferase

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Formyl-coenzyme A transferase

Function / homology

Transferases; Transferring sulfur-containing groups; CoA-transferases / CoA-transferase activity / : / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / SUCCINIC ACID / Formyl-coenzyme a transferase

Function and homology information

Biological species

Brucella melitensis 16M1W (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.88 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with succinate
Authors: Liu, L. / Lovell, S. / Cooper, A. / Battaile, K.P.

History

Deposition	Nov 19, 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	9zav.cif.gz	759.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9zav.ent.gz	634.6 KB	Display	PDB format
PDBx/mmJSON format	9zav.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9zav_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9zav_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9zav_validation.xml.gz	73.8 KB	Display
Data in CIF	9zav_validation.cif.gz	94.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/za/9zav ftp://data.pdbj.org/pub/pdb/validation_reports/za/9zav	HTTPS FTP

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Related structure data

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

Deposited unit

A: Formyl-coenzyme a transferase

B: Formyl-coenzyme a transferase

C: Formyl-coenzyme a transferase

D: Formyl-coenzyme a transferase

E: Formyl-coenzyme a transferase

hetero molecules

221 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Formyl-coenzyme a transferase

hetero molecules

A: Formyl-coenzyme a transferase

hetero molecules

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

2

B: Formyl-coenzyme a transferase

C: Formyl-coenzyme a transferase

hetero molecules

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

3

D: Formyl-coenzyme a transferase

E: Formyl-coenzyme a transferase

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

Unit cell

Length a, b, c (Å)	189.590, 189.590, 199.316
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Formyl-coenzyme a transferase Mass: 44101.301 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis 16M1W (bacteria) / Gene: BMEII0224 / Plasmid: BrmeA.18114.b.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8YDF2, Transferases; Transferring sulfur-containing groups; CoA-transferases
#2: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₆O₄ / Feature type: SUBJECT OF INVESTIGATION
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: 4.06 Å³/Da / Density % sol: 69.71 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Index C10: 1.0M Succinic acid pH 7.0, 0.1M HEPES pH 7.0, 1% PEG 200mme. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. Succinate in 3 subunits was acquired from the crystallant. plate 19820 C10 ...Details: Index C10: 1.0M Succinic acid pH 7.0, 0.1M HEPES pH 7.0, 1% PEG 200mme. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. Succinate in 3 subunits was acquired from the crystallant. plate 19820 C10 drop 1, Puck: PSL-2010, Cryo: 20% PEG 200 + 80% crystallant

Crystal

Density Matthews: 4.06 Å³/Da / Density % sol: 69.71 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Index C10: 1.0M Succinic acid pH 7.0, 0.1M HEPES pH 7.0, 1% PEG 200mme. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. Succinate in 3 subunits was acquired from the crystallant. plate 19820 C10 ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 7, 2025
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.88→48.19 Å / Num. obs: 82434 / % possible obs: 100 % / Redundancy: 26.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.208 / R_pim(I) all: 0.041 / R_rim(I) all: 0.212 / Χ²: 1.3 / Net I/σ(I): 18 / Num. measured all: 2185858
Reflection shell	Resolution: 2.88→2.95 Å / % possible obs: 99.9 % / Redundancy: 28.5 % / R_merge(I) obs: 2.636 / Num. measured all: 171351 / Num. unique obs: 6011 / CC_1/2: 0.649 / R_pim(I) all: 0.499 / R_rim(I) all: 2.684 / Χ²: 0.95 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5819: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.88→48.19 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2252	4273	5.19 %
R_work	0.1917	-	-
obs	0.1934	82347	99.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.88→48.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15068	0	24	0	15092

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	15379
X-RAY DIFFRACTION	f_angle_d	0.62	20889
X-RAY DIFFRACTION	f_dihedral_angle_d	11.534	5625
X-RAY DIFFRACTION	f_chiral_restr	0.043	2367
X-RAY DIFFRACTION	f_plane_restr	0.007	2751

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 (%)
2.88-2.91	0.441	129	0.4352	2562	X-RAY DIFFRACTION	100
2.91-2.95	0.4611	151	0.4058	2550	X-RAY DIFFRACTION	100
2.95-2.98	0.3527	137	0.3545	2591	X-RAY DIFFRACTION	100
2.98-3.02	0.3634	153	0.3299	2551	X-RAY DIFFRACTION	100
3.02-3.06	0.3837	129	0.3238	2586	X-RAY DIFFRACTION	100
3.06-3.1	0.3568	143	0.3032	2546	X-RAY DIFFRACTION	100
3.1-3.15	0.294	132	0.2596	2586	X-RAY DIFFRACTION	100
3.15-3.19	0.2747	141	0.2473	2558	X-RAY DIFFRACTION	100
3.19-3.24	0.2664	141	0.2406	2576	X-RAY DIFFRACTION	100
3.24-3.3	0.2761	132	0.2409	2574	X-RAY DIFFRACTION	100
3.3-3.35	0.2644	125	0.255	2599	X-RAY DIFFRACTION	100
3.35-3.41	0.3003	121	0.2523	2589	X-RAY DIFFRACTION	100
3.41-3.48	0.2876	142	0.2692	2594	X-RAY DIFFRACTION	100
3.48-3.55	0.2922	129	0.2597	2577	X-RAY DIFFRACTION	100
3.55-3.63	0.2673	175	0.2242	2570	X-RAY DIFFRACTION	100
3.63-3.71	0.2466	169	0.1921	2560	X-RAY DIFFRACTION	100
3.71-3.81	0.2131	162	0.1781	2554	X-RAY DIFFRACTION	100
3.81-3.91	0.2196	168	0.1719	2550	X-RAY DIFFRACTION	100
3.91-4.02	0.2035	144	0.1654	2611	X-RAY DIFFRACTION	100
4.02-4.15	0.1783	144	0.1614	2580	X-RAY DIFFRACTION	100
4.15-4.3	0.2045	129	0.1649	2632	X-RAY DIFFRACTION	100
4.3-4.47	0.1831	152	0.1469	2586	X-RAY DIFFRACTION	100
4.47-4.68	0.1766	160	0.1353	2595	X-RAY DIFFRACTION	100
4.68-4.92	0.1617	131	0.1358	2624	X-RAY DIFFRACTION	100
4.92-5.23	0.1924	121	0.1522	2650	X-RAY DIFFRACTION	100
5.23-5.63	0.1942	121	0.1717	2655	X-RAY DIFFRACTION	100
5.63-6.2	0.2018	141	0.1745	2656	X-RAY DIFFRACTION	100
6.2-7.09	0.1928	157	0.1807	2662	X-RAY DIFFRACTION	100
7.1-8.93	0.195	122	0.1588	2724	X-RAY DIFFRACTION	100
8.93-48.19	0.2098	172	0.1772	2826	X-RAY DIFFRACTION	100

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	6.0612	1.193	-1.4739	2.0758	0.0866	0.6583	0.0683	0.2292	0.0984	-0.1893	0.0855	0.3051	-0.0993	-0.4336	-0.1666	0.5896	0.1153	-0.0095	0.5951	0.117	0.3173	-40.4316	-24.8063	-3.4766
2	3.5228	0.7228	-1.7529	3.25	-1.1639	2.7074	0.1123	0.0616	0.5014	0.2239	0.0553	0.256	-0.5311	-0.1635	-0.1905	0.6198	0.1536	-0.0202	0.5681	0.0748	0.4559	-44.9982	-14.657	0.6985
3	3.3488	0.2112	-0.6153	1.5491	0.2346	1.0095	-0.0793	-0.3377	0.2487	0.3329	0.0979	-0.0236	-0.0776	0.0442	-0.0126	0.6617	0.0542	-0.0335	0.5927	0.0385	0.3791	-30.4734	-22.6751	9.653
4	1.9557	-0.5355	-1.4306	1.6113	-0.4382	2.4985	0.1483	-0.1171	0.1348	-0.0725	-0.07	-0.4646	0.0307	0.5301	-0.0988	0.462	-0.0057	-0.0048	0.6425	0.0605	0.552	-0.9758	-24.1514	-10.3134
5	2.7358	-0.5732	-1.071	2.0001	-0.8532	2.3549	0.0953	0.5865	0.1045	-0.1195	0.1333	0.4245	-0.243	-0.4538	-0.2471	0.6199	0.0793	-0.1034	0.7346	0.1472	0.5346	-46.8309	-17.0489	-10.242
6	4.0473	-0.9275	-0.1718	5.5706	-1.3094	1.6541	-0.393	-0.2545	0.2633	0.0188	0.6137	0.7212	-0.1167	-0.2237	-0.226	0.5899	0.099	-0.0507	0.7378	0.1653	0.3831	0.21	114.7481	15.3325
7	1.5447	-0.3817	-0.4509	3.9102	-0.3641	2.7074	-0.5189	-1.2641	0.3228	1.4972	0.517	0.6184	-0.2173	-0.236	-0.1031	1.0416	0.2283	0.1878	1.0164	0.1118	0.5475	0.2444	109.9408	30.4124
8	2.4	-0.8756	0.4091	4.5658	-1.1302	1.6072	-0.2991	-0.3577	-0.1714	0.6914	0.4102	0.1318	-0.0665	-0.2693	-0.0756	0.665	0.0484	-0.0072	0.7399	0.0824	0.2667	13.6105	100.1771	22.5755
9	4.6811	-2.0509	-2.0998	5.021	0.1372	4.9968	-0.1234	-0.1473	-0.2977	0.0668	0.1082	-0.655	0.5394	0.319	0.006	0.5325	0.0799	0.008	0.5544	0.0145	0.6369	36.6125	84.4432	9.8195
10	1.026	-0.7349	-0.5817	4.4257	2.0382	1.0307	0.6254	0.7368	0.0852	-0.4153	-0.4515	-1.2244	-0.4147	-0.285	-0.2408	0.7404	-0.0116	0.1223	0.812	0.0766	0.5017	27.9583	94.7325	-3.6307
11	2.7369	-1.5864	-0.4039	3.5834	-0.458	0.8215	0.1098	0.14	0.0816	-0.3291	0.1757	0.6089	0.1993	-0.4597	-0.2741	0.6493	0.0458	-0.1605	0.8674	0.2231	0.497	-2.302	116.3124	5.3917
12	6.027	-1.5829	1.9319	6.5357	-1.5335	2.5471	-0.2255	-0.3873	-0.8143	-0.2693	0.4918	0.5208	0.3781	-0.1105	-0.2191	0.7096	-0.0514	0.0431	0.5387	0.1417	0.4598	12.3211	80.0718	18.8365
13	2.3391	1.5319	0.9667	6.5768	0.0066	1.8525	-0.22	0.5036	-0.5816	-1.432	0.364	0.2674	0.5837	-0.1023	-0.1	1.0476	-0.1367	-0.1679	0.7071	0.0028	0.6174	6.8718	79.2561	3.4839
14	1.7225	0.3049	0.4242	4.5374	-0.5101	1.7489	-0.1297	0.1549	-0.0256	-0.5974	0.1433	-0.17	0.2137	0.0207	-0.0086	0.6462	-0.0145	0.0106	0.685	0.0775	0.2959	16.8434	102.2309	10.0615
15	6.1575	0.208	0.9662	7.3122	-1.1838	6.742	0.0366	-0.035	0.5408	0.1196	0.1378	-0.1082	-0.6179	-0.0058	-0.1946	0.5826	0.0003	-0.0886	0.4958	-0.0314	0.4823	25.6072	126.4964	24.8019
16	0.6785	-0.3949	-0.7084	1.5421	0.5467	0.4918	0.4264	-0.3548	0.2315	0.6971	-0.2136	-0.7733	0.7011	0.274	-0.1122	0.8489	0.0733	-0.2064	0.9019	0.0521	0.4903	22.9561	109.8384	35.0912
17	1.6165	0.41	0.5657	4.1249	-0.114	0.8105	0.0659	-0.1814	-0.6477	0.2617	0.145	0.1384	0.0016	-0.2279	-0.1825	0.8229	-0.0349	0.0902	0.7272	0.2834	0.7132	9.1757	75.2074	25.7309
18	3.2291	0.0038	0.4437	2.1988	0.0474	1.3185	0.1142	0.2896	-0.1943	-0.5297	-0.1046	-0.5565	0.278	0.2672	-0.0286	0.7051	0.0354	0.1175	0.5189	-0.0098	0.5945	8.2477	12.0218	27.188
19	2.6757	-0.2208	-0.4989	0.6476	1.4154	2.7317	0.3585	0.0452	0.1275	0.0871	0.0756	-1.2929	-0.5662	1.1632	-0.3137	1.0411	-0.2632	0.087	1.2098	0.1315	1.7989	37.4814	34.0984	36.9922
20	0.0812	-0.0391	-0.0432	-0.0206	-0.0695	0.1367	0.3992	-0.5161	0.6252	0.7523	-0.5056	0.1337	-0.4634	0.9228	0.1014	1.3976	-0.3204	-0.0915	1.8066	0.0971	2.616	47.3287	38.4463	41.6598
21	0.3859	-0.7496	0.097	2.268	0.3252	1.3299	-0.0386	-0.1861	0.1638	0.286	-0.0466	-0.4231	0.144	0.1849	0.108	0.7204	-0.0289	-0.0593	0.75	0.0449	0.8426	12.1068	11.5045	45.4415
22	2.098	-0.3073	0.262	3.214	-0.3527	1.3011	0.1081	0.0465	0.4028	0.032	-0.2217	-0.9019	-0.1997	0.3181	0.0896	0.5413	-0.0979	0.0525	0.5379	0.0501	0.7801	14.107	35.1047	36.0979
23	2.7305	-0.9074	-0.3185	1.0298	2.5959	6.0624	0.5729	0.295	-0.3176	-0.079	0.2163	-1.1082	0.8404	0.1099	-0.8173	1.088	0.0828	0.1487	0.9094	0.0507	1.6323	30.2639	1.9517	23.1828
24	1.0992	-0.5635	0.146	1.2271	0.4145	0.7516	0.5813	0.5394	-0.0505	-1.0062	-0.5277	-0.6647	0.5474	0.7215	-0.0144	1.2388	0.3218	0.4324	1.2936	-0.1066	1.5482	31.7585	3.8775	15.4971
25	0.9715	-0.3488	0.1813	5.1897	0.6243	1.2752	0.1514	0.4239	0.3657	-0.8741	-0.2294	-0.5779	-0.027	0.0321	-0.0285	0.8278	0.0065	0.248	0.7402	0.147	0.9436	10.8066	43.0357	19.8735

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 48 through 76 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 77 through 148 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 149 through 264 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 265 through 379 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 380 through 450 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 49 through 148 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 149 through 187 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 188 through 264 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 265 through 345 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 346 through 379 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 380 through 450 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 49 through 124 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 125 through 187 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 188 through 287 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 288 through 345 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 346 through 380 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 381 through 450 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 49 through 264 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 265 through 309 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 310 through 345 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 346 through 450 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 49 through 264 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 265 through 318 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 319 through 373 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 374 through 450 )

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About Yorodumi

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Yorodumi