PDB-10ui: Crystal structure of Formyl-coenzyme A transferase from Brucella ...

ID or keywords:

Entry

Database: PDB / ID: 10ui

Title

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

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 / DI(HYDROXYETHYL)ETHER / Formyl-coenzyme a transferase

Function and homology information

Biological species

Brucella melitensis 16M1W (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.34 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 Zinc
Authors: Liu, L. / Lovell, S. / Cooper, A. / Battaile, K.P.

History

Deposition	Feb 9, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 18, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	10ui.cif.gz	617.6 KB	Display	PDBx/mmCIF format
PDB format	pdb10ui.ent.gz	511.3 KB	Display	PDB format
PDBx/mmJSON format	10ui.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/0u/10ui ftp://data.pdbj.org/pub/pdb/validation_reports/0u/10ui	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

hetero molecules

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

1

A: Formyl-coenzyme a transferase

B: Formyl-coenzyme a transferase

hetero molecules

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

2

C: Formyl-coenzyme a transferase

D: Formyl-coenzyme a transferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.267, 127.954, 224.323
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Formyl-coenzyme a transferase Mass: 44101.301 Da / Num. of mol.: 4 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-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.21 Å³/Da / Density % sol: 44.28 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PPX D8: 0.2M Magnesium Acetate, 0.1M MES pH 6.5, 15% PEG 6000. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. plate 19824 D8 drop 1, Puck: PSL-1911, Cryo: 20% PEG 200 + 80% crystallant

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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: Apr 5, 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: 2.34→48.85 Å / Num. obs: 67116 / % possible obs: 100 % / Redundancy: 13.2 % / CC_1/2: 0.997 / R_merge(I) obs: 0.268 / R_pim(I) all: 0.076 / R_rim(I) all: 0.279 / Χ²: 1.14 / Net I/σ(I): 11.3 / Num. measured all: 889071
Reflection shell	Resolution: 2.34→2.4 Å / % possible obs: 100 % / Redundancy: 12.8 % / R_merge(I) obs: 2.036 / Num. measured all: 62410 / Num. unique obs: 4893 / CC_1/2: 0.487 / R_pim(I) all: 0.592 / R_rim(I) all: 2.122 / Χ²: 0.98 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5936: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.34→48.85 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2626	3416	5.1 %
R_work	0.2168	-	-
obs	0.2192	67016	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.34→48.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12107	0	18	132	12257

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	12384
X-RAY DIFFRACTION	f_angle_d	0.623	16814
X-RAY DIFFRACTION	f_dihedral_angle_d	17.105	4560
X-RAY DIFFRACTION	f_chiral_restr	0.043	1904
X-RAY DIFFRACTION	f_plane_restr	0.006	2210

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 (%)
2.34-2.37	0.3791	137	0.3204	2634	X-RAY DIFFRACTION	100
2.37-2.41	0.3553	153	0.2965	2569	X-RAY DIFFRACTION	100
2.41-2.45	0.3417	139	0.2931	2647	X-RAY DIFFRACTION	100
2.45-2.49	0.3325	129	0.2895	2617	X-RAY DIFFRACTION	100
2.49-2.53	0.3355	136	0.2865	2592	X-RAY DIFFRACTION	100
2.53-2.58	0.2999	122	0.291	2675	X-RAY DIFFRACTION	100
2.58-2.63	0.33	131	0.2917	2596	X-RAY DIFFRACTION	100
2.63-2.68	0.3955	176	0.2725	2570	X-RAY DIFFRACTION	100
2.68-2.74	0.3138	148	0.2649	2623	X-RAY DIFFRACTION	100
2.74-2.8	0.3138	137	0.2636	2632	X-RAY DIFFRACTION	100
2.8-2.87	0.3152	132	0.2481	2629	X-RAY DIFFRACTION	100
2.87-2.95	0.3188	146	0.2574	2617	X-RAY DIFFRACTION	100
2.95-3.03	0.2934	137	0.2613	2671	X-RAY DIFFRACTION	100
3.03-3.13	0.3235	146	0.2671	2588	X-RAY DIFFRACTION	100
3.13-3.24	0.2841	130	0.2582	2655	X-RAY DIFFRACTION	100
3.24-3.37	0.2952	145	0.2374	2669	X-RAY DIFFRACTION	100
3.37-3.53	0.2842	163	0.2251	2581	X-RAY DIFFRACTION	100
3.53-3.71	0.2329	139	0.2035	2666	X-RAY DIFFRACTION	100
3.71-3.95	0.2607	146	0.1857	2673	X-RAY DIFFRACTION	100
3.95-4.25	0.2256	153	0.1785	2667	X-RAY DIFFRACTION	100
4.25-4.68	0.204	145	0.16	2685	X-RAY DIFFRACTION	100
4.68-5.35	0.1896	157	0.1656	2704	X-RAY DIFFRACTION	100
5.36-6.74	0.2108	126	0.1826	2764	X-RAY DIFFRACTION	100
6.74-48.85	0.2012	143	0.1716	2876	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	0.2202	0.3221	-0.3992	1.5351	-1.0075	1.7366	0.2262	-0.1151	0.0878	0.2815	-0.0696	-0.2183	-0.7489	0.2696	-0.1086	0.5903	-0.1035	0.1639	0.2522	-0.103	0.4423	-10.9111	17.6836	4.7645
2	2.426	1.1398	0.1545	3.4571	-0.6335	0.1815	-0.11	-0.0684	0.3095	-0.0218	0.2226	-0.5917	-0.5352	0.4352	0.0036	0.7346	-0.328	0.0356	0.562	-0.1161	0.511	1.6904	18.2799	12.9766
3	0.7527	0.1689	-0.0589	0.8979	-0.267	2.3615	0.1368	-0.1447	0.1332	0.0033	0.0235	-0.1078	-0.2836	0.4868	-0.1353	0.2489	-0.0535	0.0542	0.3607	-0.0691	0.3314	-4.7709	-0.382	-2.548
4	3.5217	-0.4445	0.1111	2.6613	-0.2595	2.8546	0.0745	0.2853	-0.1278	-0.0986	0.1191	0.2754	0.5519	-0.2896	-0.2193	0.3557	-0.0801	-0.0754	0.2971	0.0769	0.325	-29.1518	-19.9294	-20.5538
5	1.1637	1.5465	0.6512	2.6573	0.7578	0.378	-0.0528	-0.2031	0.3812	-0.339	0.1204	0.6797	-0.1629	-0.3427	-0.0105	0.3151	0.0198	0.0242	0.4141	0.1225	0.5642	-34.6837	-2.1398	-13.9163
6	0.3895	-0.4567	0.3745	1.2562	0.0567	0.7062	0.2326	-0.0718	0.3309	0.1707	-0.1031	0.4205	-0.737	0.0525	-0.1343	0.6122	0.0063	0.2114	0.3105	-0.0991	0.5349	-23.6572	16.0561	5.7219
7	1.5495	1.2971	-0.2247	4.0966	-0.3956	0.0459	-0.0255	-0.223	0.3273	0.3227	-0.2055	0.3608	-0.3349	0.0547	0.2317	1.0048	-0.2583	0.1434	0.3351	-0.1657	0.6816	-6.7249	32.6456	14.1631
8	1.0256	-0.1634	-0.2638	1.5109	0.2718	2.7794	0.1836	-0.1035	0.027	0.0635	-0.0256	0.2159	0.2068	-0.1571	-0.1497	0.2373	-0.0083	-0.0237	0.2057	-0.0034	0.2802	-17.7257	-18.325	7.1596
9	0.5879	0.2397	-0.4144	0.817	-0.9034	3.0031	0.1983	-0.0243	0.1528	0.0514	0.1144	0.1925	-0.2112	-0.1859	-0.3071	0.2714	0.0264	0.0524	0.2301	-0.0065	0.3301	-23.7586	-2.8909	1.9174
10	3.2018	0.5246	0.0607	1.4715	-0.5591	1.4949	0.1606	-0.1287	0.2122	0.1574	0.0992	0.062	-0.3823	0.1852	-0.1104	0.3368	-0.0451	0.0782	0.2576	-0.0025	0.3671	-11.0291	12.7777	-17.7798
11	3.1609	-1.1399	-0.3768	2.2252	-0.3311	2.3108	0.1744	0.1162	0.3884	0.2317	-0.136	-0.3156	-0.5344	0.4085	-0.1187	0.4325	-0.1582	0.0997	0.3648	-0.0037	0.4486	1.4939	19.7832	-20.5584
12	0.3479	0.4907	-0.6221	0.9818	-0.8908	1.1464	0.1821	-0.349	-0.0824	-0.0893	-0.388	-0.2809	-0.148	0.6893	0.133	0.284	-0.0592	0.0607	0.5358	0.0043	0.3938	7.0432	1.8872	-14.7376
13	0.4229	-0.4137	-0.3273	0.6385	-0.2738	1.7776	0.2087	-0.1697	0.0345	0.0262	-0.1936	-0.3915	0.2494	0.6124	0.0531	0.2859	0.0083	-0.0028	0.4794	-0.0117	0.3594	-2.11	-16.6361	4.4183
14	3.485	1.5159	0.1183	4.0181	-0.2353	2.8228	0.0612	-0.5601	-0.6751	0.3641	-0.1688	-0.4212	0.8579	0.0751	0.038	0.5054	-0.0351	-0.0563	0.3605	0.0702	0.3231	-18.4402	-33.2183	14.4413
15	0.3637	0.7209	-0.0656	3.2093	-0.5671	1.5462	0.6722	0.2465	0.1854	-0.418	-0.8162	0.6839	-0.3799	0.3063	0.0722	0.4541	0.2355	-0.0264	0.7311	-0.1209	0.433	-17.5613	21.9831	-61.4192
16	1.3716	0.3608	0.6983	0.6749	-0.7768	2.1111	0.4267	0.26	0.0194	-0.5016	0.094	1.0666	-0.1045	-0.6573	-0.4441	0.6522	0.3121	-0.318	0.6857	-0.1217	0.9612	-30.5655	13.1805	-63.8737
17	0.0101	0.0052	-0.0707	1.5214	-0.2925	0.4878	0.4629	0.3375	-0.2005	-0.3758	-0.6049	0.9536	0.0043	0.1814	-0.0631	0.382	0.1473	-0.1007	0.5609	-0.2044	0.5474	-17.4332	-1.2513	-51.3015
18	1.4454	0.3705	0.4636	1.5617	-0.6339	0.5246	0.2494	0.3695	-0.3147	-0.1166	-0.7094	-0.875	0.0159	0.6539	0.297	0.3288	-0.0066	-0.0263	0.8612	0.2732	0.57	4.369	-11.4765	-38.9773
19	0.813	0.201	-0.4419	2.27	-0.3918	0.4711	0.6095	0.159	0.2436	-0.0327	-1.0837	-0.3522	-0.2579	0.7014	0.0785	0.5464	0.1306	0.057	0.9888	0.232	0.3707	-8.3898	27.0788	-62.6071
20	0.2397	0.1552	0.0728	0.9553	-0.6579	0.598	0.0992	0.1258	-0.128	-0.6384	-0.2073	-0.1032	0.36	0.3428	0.0916	0.9782	1.0928	-0.1293	0.6642	-0.3713	0.4368	-10.1432	-14.6916	-62.6795
21	0.3749	0.4688	-0.0352	0.809	-0.4626	0.7681	0.1896	-0.0578	-0.3661	-0.7729	-0.3759	-0.5869	0.4642	0.5481	0.0761	0.8965	0.6035	0.2038	1.224	0.1884	0.6162	3.9569	-8.7916	-67.5729
22	0.0466	0.2378	-0.1649	1.4475	-0.9195	0.5802	0.4016	0.2224	-0.1353	-0.2649	-0.7977	-0.0669	0.0023	0.8156	0.0473	0.3576	0.1591	0.024	0.8377	0.0248	0.2745	-5.7112	3.7019	-53.9225
23	3.7909	-0.4021	0.0885	0.9744	-0.798	2.1753	0.0238	-0.0417	-0.1222	-0.1432	0.1906	0.1432	-0.7572	-0.0743	-0.2544	0.4876	-0.0323	0.099	0.2602	-0.0133	0.2968	-27.4124	14.286	-37.3292
24	0.3106	0.1695	-0.2402	0.1331	0.0064	1.0026	0.0416	0.2683	-0.327	-0.4644	-0.0535	0.2942	0.4944	0.2052	-0.3285	0.9097	0.2841	-0.4335	0.5145	-0.4603	0.8147	-23.3144	-12.7095	-63.3911
25	0.3346	-0.4636	0.6268	2.3362	-1.2435	1.3178	-0.398	0.2476	-0.5222	0.1749	0.1417	0.0638	0.2692	-0.0768	0.2784	1.24	0.3377	-0.0088	0.7347	-0.1766	0.7825	-6.7697	-28.4443	-73.4851

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 48 through 124 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 125 through 148 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 149 through 288 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 289 through 345 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 346 through 379 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 380 through 420 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 421 through 450 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 48 through 148 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 149 through 264 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 265 through 288 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 289 through 345 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 346 through 379 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 380 through 420 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 421 through 450 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 49 through 148 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 149 through 187 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 188 through 287 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 288 through 379 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 380 through 450 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 50 through 124 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 125 through 187 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 188 through 264 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 265 through 379 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 380 through 420 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 421 through 450 )

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