PDB-11ef: Crystal Structure of L-erythrulose-1-phosphate isomerase from Bru...

ID or keywords:

Entry

Database: PDB / ID: 11ef

Title

Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis (P21 form)

Components

L-erythrulose-1-phosphate isomerase

Keywords

ISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / L-erythrulose-1-phosphate isomerase

Function / homology

Function and homology information

L-erythrulose-1-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / cytosol
Similarity search - Function

Biological species

Brucella abortus 2308 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

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 L-erythrulose-1-phosphate isomerase from Brucella melitensis (P21 form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Feb 18, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	11ef.cif.gz	398.5 KB	Display	PDBx/mmCIF format
PDB format	pdb11ef.ent.gz	327 KB	Display	PDB format
PDBx/mmJSON format	11ef.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/1e/11ef ftp://data.pdbj.org/pub/pdb/validation_reports/1e/11ef	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
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (6)

Deposited unit

A: L-erythrulose-1-phosphate isomerase

B: L-erythrulose-1-phosphate isomerase

C: L-erythrulose-1-phosphate isomerase

D: L-erythrulose-1-phosphate isomerase

hetero molecules

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

1

A: L-erythrulose-1-phosphate isomerase

B: L-erythrulose-1-phosphate isomerase

hetero molecules

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

2

C: L-erythrulose-1-phosphate isomerase

D: L-erythrulose-1-phosphate isomerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.668, 141.818, 94.580
Angle α, β, γ (deg.)	90.00, 96.42, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	L-erythrulose-1-phosphate isomerase / D-3-tetrulose-4-phosphate isomerase Mass: 28744.627 Da / Num. of mol.: 4 / Mutation: A173D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus 2308 (bacteria) / Gene: eryH, tpiA-2, BAB2_0367 / Plasmid: BrabA.00276.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q2YIQ6, L-erythrulose-1-phosphate isomerase

#1: Protein

L-erythrulose-1-phosphate isomerase / D-3-tetrulose-4-phosphate isomerase

Mass: 28744.627 Da / Num. of mol.: 4 / Mutation: A173D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Brucella abortus 2308 (bacteria) / Gene: eryH, tpiA-2, BAB2_0367 / Plasmid: BrabA.00276.a.B2 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2YIQ6, L-erythrulose-1-phosphate isomerase

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Non-polymers , 5 types, 429 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.88 Å³/Da / Density % sol: 57.28 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: JCSG+ D12: 40 mM potassium phosphate, 16% PEG 8000, 20% glycerol. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. plate 20694 D12 drop 1, Puck: PSL-1811, Cryo: JCSG+ D12.

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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: Jan 31, 2026
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: 2.15→49.36 Å / Num. obs: 70493 / % possible obs: 100 % / Redundancy: 7 % / CC_1/2: 0.996 / R_merge(I) obs: 0.168 / R_pim(I) all: 0.068 / R_rim(I) all: 0.181 / Χ²: 1.12 / Net I/σ(I): 9.2 / Num. measured all: 492483
Reflection shell	Resolution: 2.15→2.21 Å / % possible obs: 100 % / Redundancy: 7.1 % / R_merge(I) obs: 1.292 / Num. measured all: 36696 / Num. unique obs: 5147 / CC_1/2: 0.775 / R_pim(I) all: 0.518 / R_rim(I) all: 1.393 / 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: 2.15→46.61 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.218	3562	5.06 %
R_work	0.1794	-	-
obs	0.1813	70417	99.9 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.15→46.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7592	0	60	413	8065

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7808
X-RAY DIFFRACTION	f_angle_d	0.711	10594
X-RAY DIFFRACTION	f_dihedral_angle_d	14.156	2840
X-RAY DIFFRACTION	f_chiral_restr	0.047	1188
X-RAY DIFFRACTION	f_plane_restr	0.007	1372

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 (%)
2.15-2.18	0.346	146	0.2725	2625	X-RAY DIFFRACTION	100
2.18-2.21	0.3006	148	0.2609	2647	X-RAY DIFFRACTION	100
2.21-2.24	0.2644	120	0.2511	2695	X-RAY DIFFRACTION	100
2.24-2.28	0.3337	153	0.239	2650	X-RAY DIFFRACTION	100
2.28-2.32	0.2783	157	0.2251	2639	X-RAY DIFFRACTION	100
2.32-2.36	0.2774	143	0.2218	2687	X-RAY DIFFRACTION	100
2.36-2.4	0.2487	122	0.2211	2644	X-RAY DIFFRACTION	100
2.4-2.44	0.2707	142	0.216	2677	X-RAY DIFFRACTION	100
2.44-2.49	0.2474	135	0.2138	2738	X-RAY DIFFRACTION	100
2.49-2.55	0.265	151	0.211	2620	X-RAY DIFFRACTION	100
2.55-2.61	0.2217	141	0.2032	2693	X-RAY DIFFRACTION	100
2.61-2.67	0.2446	141	0.2006	2653	X-RAY DIFFRACTION	100
2.67-2.75	0.2342	140	0.1909	2689	X-RAY DIFFRACTION	100
2.75-2.83	0.2358	141	0.1895	2643	X-RAY DIFFRACTION	100
2.83-2.92	0.2414	148	0.1866	2694	X-RAY DIFFRACTION	100
2.92-3.02	0.2556	135	0.1882	2659	X-RAY DIFFRACTION	100
3.02-3.14	0.2488	155	0.1986	2682	X-RAY DIFFRACTION	100
3.14-3.29	0.2444	129	0.1803	2712	X-RAY DIFFRACTION	100
3.29-3.46	0.2141	149	0.1652	2627	X-RAY DIFFRACTION	100
3.46-3.68	0.1882	146	0.1688	2692	X-RAY DIFFRACTION	100
3.68-3.96	0.1947	125	0.1591	2705	X-RAY DIFFRACTION	100
3.96-4.36	0.166	152	0.1409	2658	X-RAY DIFFRACTION	100
4.36-4.99	0.1527	146	0.1312	2721	X-RAY DIFFRACTION	100
4.99-6.28	0.181	142	0.1653	2694	X-RAY DIFFRACTION	100
6.28-46.61	0.2016	155	0.1659	2711	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	6.834	-1.6846	2.6613	3.4167	-1.9738	1.8533	-0.2669	0.0823	0.7814	0.0494	0.127	-0.1094	-0.1722	0.1066	0.1025	0.2791	-0.0392	-0.0266	0.3227	-0.0537	0.331	14.8351	3.9804	30.9722
2	1.1969	0.6944	-0.237	2.8696	0.0703	1.2048	-0.032	-0.0674	0.1045	0.0478	-0.0596	0.0605	-0.1069	-0.089	0.0901	0.2299	0.0104	-0.0014	0.3143	-0.032	0.2615	16.5824	-0.1566	38.8973
3	2.3167	-0.4876	-0.3317	1.8724	-0.3497	3.9304	0.1023	0.3505	-0.2179	-0.1667	0.0343	0.027	-0.0558	-0.268	-0.1473	0.2622	-0.0241	0.0088	0.4558	-0.0645	0.2993	3.5978	-9.1348	28.8207
4	9.0672	-3.431	4.3484	3.8439	-0.4912	2.6101	0.3489	0.5629	0.212	-0.201	-0.2731	0.3355	0.8499	-0.6145	-0.0896	0.2999	0.0025	0.0352	0.479	-0.0088	0.4343	-5.8856	-8.0342	26.8225
5	1.8615	0.7503	0.7413	4.1137	-2.5716	7.8847	-0.0075	0.1517	0.0928	-0.1793	0.123	-0.0353	-0.1932	-0.1666	-0.0971	0.2502	0.0314	0.028	0.4029	-0.1232	0.3742	-0.3354	-2.3198	31.1663
6	4.0494	2.7194	-2.1786	3.2231	-2.6708	2.8394	0.0831	0.1382	0.3025	-0.0742	0.0905	0.2436	-0.206	-0.1972	-0.1764	0.3253	0.0719	-0.0161	0.3903	-0.037	0.3067	-2.8234	4.1254	27.1371
7	9.7289	-0.649	1.2971	4.79	-1.571	3.2665	0.0296	0.2948	0.515	-0.2589	-0.1936	0.1087	-0.3332	0.1997	0.17	0.3449	0.017	-0.0365	0.3601	0.0006	0.2656	7.3515	9.5896	25.1127
8	2.3677	-2.89	2.0991	4.6148	-2.1181	2.3054	-0.1331	0.23	0.8786	-0.1694	0.0691	-0.0253	-0.8323	0.1567	0.0462	0.5452	-0.0234	-0.0347	0.4214	0.0152	0.5291	12.4836	16.9395	28.2163
9	2.2679	-1.8829	-0.9038	5.3915	2.3604	3.9944	0.0979	-0.5002	0.1781	-0.0237	0.1581	-0.2174	-0.0097	0.3737	-0.2279	0.2501	-0.0487	0.0162	0.3581	-0.012	0.3126	27.9901	-23.3099	41.5661
10	9.7398	-5.7397	1.7361	4.9804	0.0672	3.0195	0.0122	-1.0039	0.0406	0.3109	0.2664	0.0615	0.0724	0.2286	-0.2	0.3058	-0.0214	0.0172	0.4278	-0.0432	0.2522	31.1447	-15.1132	50.6255
11	2.2997	-0.4976	1.0369	1.3186	-1.0125	2.6056	0.0656	0.0622	0.0076	-0.0998	-0.0477	-0.1787	0.1439	0.2543	-0.012	0.2131	0.0061	0.0321	0.3176	-0.0561	0.2541	30.5483	-15.368	35.6892
12	5.1541	1.5925	-0.9049	3.1633	0.7142	2.8456	-0.0711	0.4612	0.0261	-0.1597	0.0516	0.2946	0.241	-0.092	0.043	0.3503	0.0142	0.0019	0.3605	-0.0573	0.3003	21.6807	-20.5379	24.5726
13	1.605	1.2368	-0.0299	4.3766	-0.4761	0.1707	0.036	0.1117	0.0052	-0.0607	-0.0091	0.4147	0.127	0.1347	-0.0223	0.3491	0.0305	0.0316	0.3721	-0.0519	0.3755	21.1612	-33.4991	24.7702
14	0.3735	0.0407	0.7614	6.0058	-2.2507	3.4343	-0.0664	0.1794	0.0099	-0.2182	0.2507	0.2772	0.093	-0.2396	-0.1284	0.277	0.0728	0.0354	0.3997	-0.0948	0.3288	27.4777	-29.5817	26.2807
15	0.7391	0.335	-0.4735	2.7647	-0.2379	3.1645	-0.0363	-0.0213	-0.3753	-0.0953	0.0016	-0.27	0.079	0.1813	0.019	0.2748	0.0437	0.0233	0.3455	-0.056	0.3997	29.9694	-36.8806	30.1143
16	4.7491	-2.4093	-2.03	2.751	3.8038	7.3524	-0.2054	-0.0929	-0.2973	0.5498	0.2648	0.176	0.5606	0.0892	-0.0679	0.33	0.0134	0.0161	0.2785	0.0015	0.3156	29.3017	-34.1856	41.3518
17	3.3457	-2.5154	0.6023	2.599	-0.0452	5.7901	-0.0637	-0.5167	-0.4119	0.8832	0.3598	-0.3248	0.8603	-0.1552	-0.2953	0.4269	0.0423	-0.0394	0.4469	0.0544	0.3486	34.8032	-32.3947	48.8109
18	0.9236	-1.0571	-0.7757	4.7	-0.7173	1.7471	0.0928	0.1851	-0.1036	-0.0942	-0.1166	-0.0168	0.1059	0.0685	0.0181	0.2287	-0.0001	-0.0129	0.3742	-0.0534	0.211	23.887	-5.6475	63.1668
19	2	-0.2898	-0.0734	1.1191	0.1708	1.957	0.025	0.0073	0.118	0.0164	-0.0628	-0.094	-0.1348	0.1381	0.0317	0.2059	-0.0188	-0.02	0.2948	-0.0059	0.2464	22.5065	-1.8845	75.7484
20	2.1547	-1.7064	0.9688	3.816	-2.3013	2.2437	0.0138	-0.0274	0.1687	0.0965	0.2376	0.1425	-0.1734	-0.1784	-0.2802	0.3118	-0.0429	-0.0177	0.3022	0.0208	0.3436	16.029	15.8168	75.0948
21	1.3185	-0.4638	0.1678	1.7204	0.3209	2.097	0.0355	0.161	0.1753	-0.0779	-0.0919	-0.1221	-0.1703	-0.0016	0.0623	0.2183	-0.0612	-0.0068	0.2876	0.0234	0.2818	24.3709	11.963	66.2648
22	4.3695	-0.0174	-1.1902	2.8855	-0.0561	1.4886	0.0556	-0.2735	-0.5089	0.0437	-0.0433	-0.1847	0.1312	0.1349	-0.0084	0.3127	0.0074	-0.0423	0.3553	0.0344	0.3159	14.258	-21.9936	86.2103
23	2.3359	-0.2146	0.1086	2.4414	-0.9347	2.2385	-0.0258	-0.0611	-0.4312	-0.1028	0.0113	-0.0176	0.2101	-0.0625	0.0075	0.2641	-0.0103	-0.012	0.3255	-0.0229	0.3404	9.2662	-18.4211	77.1679
24	4.0854	0.8083	1.9064	5.5085	2.3147	3.3461	-0.1382	-0.226	0.2385	-0.1685	-0.0278	0.252	-0.3097	-0.2235	0.2108	0.2433	0.0114	0.0285	0.3455	0.0025	0.2752	0.4549	-6.1875	77.9907
25	4.4606	-1.7708	-2.5881	6.2558	5.1033	7.3729	0.3608	-0.4175	0.304	0.0088	-0.4009	0.1072	-0.288	-0.5771	0.0514	0.2838	-0.0419	0.0017	0.3892	-0.0366	0.2944	-5.2646	-7.3478	90.1269
26	2.5804	-0.7701	-0.794	3.222	1.7094	5.6535	0.0524	-0.2561	-0.0248	0.2499	-0.0147	0.1563	0.1216	-0.1009	-0.0265	0.2	-0.0441	0.0313	0.3879	0.0016	0.3388	-7.4519	-11.7313	84.4693
27	3.8663	-0.127	0.7605	1.0681	-0.0619	3.4465	0.1506	-0.4887	-0.2935	0.225	-0.0905	-0.0032	0.2272	-0.1819	-0.0768	0.3175	-0.072	0.0113	0.454	0.0443	0.3361	-8.5577	-17.4643	90.6405
28	6.9262	2.082	-1.6158	2.7746	-1.2913	3.963	0.4298	-0.5651	-0.3996	0.3201	-0.3535	-0.0074	0.132	0.2264	-0.0878	0.4165	-0.0403	0.0041	0.5743	0.091	0.3505	1.6144	-21.3363	95.1195
29	8.916	2.1419	-5.6126	8.2584	-1.8344	3.592	-0.0018	-1.121	-1.0662	0.5958	-0.0579	-0.1465	0.0576	-0.1657	-0.017	0.3576	-0.0405	-0.0589	0.5688	0.228	0.5125	6.8438	-29.2086	96.0377

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 96 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 97 through 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 151 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 152 through 182 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 183 through 217 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 218 through 238 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 239 through 254 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 3 through 15 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 16 through 28 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 29 through 96 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 97 through 120 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 121 through 151 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 152 through 182 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 183 through 217 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 218 through 238 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 239 through 254 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 3 through 28 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 29 through 119 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 120 through 151 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 152 through 254 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 3 through 28 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 29 through 96 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 97 through 120 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 121 through 139 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 140 through 182 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 183 through 217 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 218 through 238 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 239 through 254 )

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