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

ID or keywords:

Entry

Database: PDB / ID: 11eg

Title

Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis (P1 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: 1.6 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 (P1 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	11eg.cif.gz	409.1 KB	Display	PDBx/mmCIF format
PDB format	pdb11eg.ent.gz	332.2 KB	Display	PDB format
PDBx/mmJSON format	11eg.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/11eg ftp://data.pdbj.org/pub/pdb/validation_reports/1e/11eg	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

115 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
57.7 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
57.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	45.259, 49.359, 116.827
Angle α, β, γ (deg.)	88.41, 83.15, 86.23
Int Tables number	1
Space group name H-M	P1

#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
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1086 / Source method: isolated from a natural source / Formula: H₂O
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: 2.25 Å³/Da / Density % sol: 45.29 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Berkeley B2: 100 mM HEPES, pH 7.5, 400 mM NaCl, 30% PEG 3350. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. plate 20692 B2 drop 1, Puck: PSL-2008, Cryo: Berkeley B2.

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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: 1.6→49.24 Å / Num. obs: 125292 / % possible obs: 94.8 % / Redundancy: 3.6 % / CC_1/2: 0.997 / R_merge(I) obs: 0.084 / R_pim(I) all: 0.052 / R_rim(I) all: 0.099 / Χ²: 0.99 / Net I/σ(I): 9.5 / Num. measured all: 449107
Reflection shell	Resolution: 1.6→1.64 Å / % possible obs: 78.3 % / Redundancy: 3.3 % / R_merge(I) obs: 0.66 / Num. measured all: 25173 / Num. unique obs: 7690 / CC_1/2: 0.652 / R_pim(I) all: 0.435 / R_rim(I) all: 0.795 / Χ²: 0.86 / 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: 1.6→49.24 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1828	6056	4.83 %
R_work	0.1555	-	-
obs	0.1568	125272	94.75 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→49.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7554	0	14	1086	8654

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7849
X-RAY DIFFRACTION	f_angle_d	0.736	10668
X-RAY DIFFRACTION	f_dihedral_angle_d	16.562	2903
X-RAY DIFFRACTION	f_chiral_restr	0.047	1197
X-RAY DIFFRACTION	f_plane_restr	0.008	1394

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 (%)
1.6-1.62	0.2994	169	0.2577	2994	X-RAY DIFFRACTION	71
1.62-1.64	0.2983	158	0.2602	3460	X-RAY DIFFRACTION	83
1.64-1.66	0.2736	196	0.2452	3795	X-RAY DIFFRACTION	90
1.66-1.68	0.2653	195	0.2342	3867	X-RAY DIFFRACTION	92
1.68-1.7	0.2389	186	0.2211	3905	X-RAY DIFFRACTION	93
1.7-1.72	0.2517	214	0.2076	3965	X-RAY DIFFRACTION	95
1.72-1.75	0.2569	197	0.1953	4058	X-RAY DIFFRACTION	96
1.75-1.77	0.2299	219	0.1882	3975	X-RAY DIFFRACTION	96
1.77-1.8	0.2021	206	0.1823	4032	X-RAY DIFFRACTION	96
1.8-1.83	0.2237	197	0.1778	4054	X-RAY DIFFRACTION	96
1.83-1.86	0.2197	202	0.1756	3968	X-RAY DIFFRACTION	96
1.86-1.9	0.1948	224	0.1686	4076	X-RAY DIFFRACTION	96
1.9-1.93	0.2092	189	0.1702	4009	X-RAY DIFFRACTION	96
1.93-1.97	0.2063	251	0.1671	4089	X-RAY DIFFRACTION	97
1.97-2.02	0.206	179	0.1734	3968	X-RAY DIFFRACTION	96
2.02-2.06	0.2057	206	0.1574	4116	X-RAY DIFFRACTION	96
2.06-2.11	0.1888	177	0.1453	4009	X-RAY DIFFRACTION	96
2.11-2.17	0.1755	195	0.1444	4099	X-RAY DIFFRACTION	97
2.17-2.24	0.1842	215	0.1424	4043	X-RAY DIFFRACTION	96
2.24-2.31	0.176	229	0.135	3979	X-RAY DIFFRACTION	97
2.31-2.39	0.1657	232	0.1425	4110	X-RAY DIFFRACTION	97
2.39-2.49	0.1914	183	0.1437	4055	X-RAY DIFFRACTION	97
2.49-2.6	0.1771	213	0.1474	4053	X-RAY DIFFRACTION	97
2.6-2.74	0.2057	168	0.1523	4076	X-RAY DIFFRACTION	97
2.74-2.91	0.1908	191	0.1555	4121	X-RAY DIFFRACTION	98
2.91-3.13	0.1737	227	0.1535	4036	X-RAY DIFFRACTION	97
3.13-3.45	0.165	203	0.1447	4095	X-RAY DIFFRACTION	97
3.45-3.95	0.136	204	0.1333	4037	X-RAY DIFFRACTION	97
3.95-4.97	0.135	205	0.1214	4086	X-RAY DIFFRACTION	96
4.97-49.24	0.175	226	0.1664	4086	X-RAY DIFFRACTION	98

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	0.5027	0.1377	-0.0261	0.9571	0.0436	0.8134	0.0161	-0.0034	-0.0216	-0.0816	-0.0313	0.0787	-0.0009	-0.0258	0.0133	0.1218	0.0028	-0.0179	0.1086	-0.0002	0.106	-4.2415	7.2248	1.7691
2	3.4861	-0.1882	-0.7468	2.5916	-0.0857	2.7138	0.0369	-0.1156	-0.2353	-0.0854	-0.0787	-0.5939	0.1615	0.5172	-0.0082	0.1618	0.0095	-0.0065	0.1991	0.0158	0.2522	6.7698	-9.1697	4.6955
3	1.1326	0.5411	-0.6131	1.8821	-0.4468	1.1671	-0.0392	0.0374	-0.1011	-0.229	-0.0193	-0.1634	0.097	0.086	0.0659	0.1685	0.0155	-0.0022	0.1385	-0.0013	0.1438	2.1156	-6.9561	-4.6988
4	3.1539	-1.9921	-1.9311	2.9061	4.3064	7.119	0.0504	0.2156	0.018	-0.49	-0.072	-0.2048	0.0851	0.0823	0.0668	0.3009	0.013	-0.0009	0.1841	0.0209	0.1448	1.8095	4.7672	-18.1274
5	2.3623	0.2233	0.7519	2.5676	0.8058	3.1409	-0.1191	-0.1708	0.1855	0.0378	0.0377	0.036	-0.249	0.121	0.0783	0.1319	-0.0008	0.0093	0.1495	-0.0072	0.0963	-3.9092	22.9067	24.7323
6	2.4872	-0.3268	0.1664	1.9202	-0.2043	1.2414	-0.0796	-0.1556	0.2461	0.2263	0.0391	0.1439	-0.1579	-0.0761	0.0616	0.1477	0.009	0.0156	0.1181	-0.0168	0.119	-10.8093	27.7339	20.6859
7	1.5349	-1.8406	-0.6575	2.8766	0.3543	1.1936	0.0384	0.0132	0.0763	0.0126	-0.0046	0.0202	-0.051	0.005	-0.0366	0.128	-0.0106	0.0035	0.1388	0.0002	0.1312	-4.1212	24.0452	13.6776
8	0.7515	-0.0655	0.1251	0.5648	0.0885	0.9333	0.0108	-0.0242	-0.0594	0.0257	0.0097	-0.021	0.069	0.0631	-0.0194	0.1381	-0.0002	-0.0022	0.1528	0.0062	0.139	7.8439	16.0779	14.46
9	0.3866	-0.4453	0.7704	2.8434	-3.6291	5.2261	0.0287	-0.0688	0.0265	-0.1581	0.0115	0.0476	0.3794	-0.102	-0.0332	0.2113	-0.0102	-0.0046	0.1973	-0.0091	0.1304	9.0933	12.9191	30.2605
10	1.1644	0.1202	-0.5426	3.6185	-2.7762	4.5062	0.0741	-0.1701	0.0033	0.2043	-0.2136	-0.1263	0.0777	0.3592	0.1672	0.1324	-0.0102	-0.0209	0.2095	-0.0063	0.1225	17.8891	20.3521	25.8845
11	2.3309	-0.5622	0.0617	1.3098	1.3579	2.5557	0.1613	-0.2726	-0.3431	0.3881	-0.125	0.1409	0.4331	-0.103	-0.0713	0.2241	-0.0435	-0.0288	0.2135	0.0005	0.1744	4.4931	15.3398	32.708
12	2.122	0.2986	0.0667	0.578	-0.0647	0.9168	0.0297	-0.1735	0.0518	0.1085	-0.0142	0.0378	-0.0224	-0.0721	-0.0103	0.2168	-0.0326	-0.0072	0.2323	-0.0044	0.1302	7.2557	22.0291	35.6621
13	2.869	0.4374	1.4697	0.9636	0.3793	2.827	0.05	-0.4811	0.0673	0.1903	-0.006	0.0471	-0.0315	-0.0684	-0.0716	0.1861	0.0013	0.0129	0.2337	0.0035	0.1052	-4.1578	21.8915	34.3029
14	2.4209	0.2448	1.3536	4.5853	1.5911	7.7946	0.0255	-0.4074	0.4036	0.2775	0.0262	0.2856	-0.1267	-0.3255	-0.0691	0.1765	0.0287	0.0685	0.2747	-0.0337	0.1883	-11.4305	27.8386	33.4941
15	1.6748	1.0349	0.501	1.9998	0.0418	1.2164	0.0717	-0.1212	-0.0755	0.1763	-0.0877	0.0114	0.0044	-0.0392	0.0093	0.1145	0.0117	0.0085	0.1356	-0.0009	0.1339	-2.8074	4.7101	-40.4832
16	1.2355	0.2688	0.0808	0.7387	-0.0978	0.7846	0.0111	0.0516	-0.0897	0.001	-0.0188	-0.0542	0.0333	0.0301	0.011	0.1101	0.0115	0.0056	0.102	-0.0106	0.1065	9.1319	5.3077	-46.4571
17	1.644	-0.9921	0.9602	1.2398	-0.7954	1.1623	-0.0366	0.1035	0.0928	-0.0615	-0.0559	-0.0374	-0.1108	0.0371	0.0991	0.1667	-0.0022	-0.0141	0.1793	-0.0118	0.1484	6.194	12.2584	-63.7654
18	2.9536	0.0948	1.5409	1.4074	-0.4344	3.1518	-0.0474	0.2179	0.0991	-0.1516	-0.0487	0.0522	-0.0835	-0.0766	0.0669	0.1645	-0.0039	0.0074	0.1405	-0.0203	0.1223	4.1317	5.1412	-64.0884
19	1.8821	-0.2579	-0.8143	0.9994	0.3033	2.7633	0.0028	0.219	-0.0219	-0.0063	-0.0352	0.1029	-0.0283	-0.2822	0.0475	0.1166	0.0102	-0.0033	0.1921	-0.014	0.1392	-6.0868	4.4133	-56.9196
20	6.4847	0.462	1.4478	5.9789	-0.2127	4.7202	-0.2546	-0.0105	-0.254	-0.1445	0.098	0.3467	0.0429	-0.4231	0.1984	0.1032	-0.0089	0.0261	0.1765	0.0063	0.1795	-13.1413	-0.0116	-49.1976
21	1.6273	0.745	0.5612	2.1197	-0.024	1.618	0.0489	-0.1347	-0.0143	0.2083	-0.0479	-0.1158	0.0663	-0.0244	0.0163	0.1364	0.0093	-0.0115	0.1262	-0.0011	0.1301	22.8714	12.5266	-28.0356
22	0.977	-0.0472	0.1265	0.9924	-0.2509	1.0575	0.0141	-0.0806	0.0417	0.0912	-0.0039	0.0125	-0.0803	-0.0499	-0.0065	0.129	0.006	0.0021	0.1009	-0.0117	0.1046	13.7889	20.4166	-33.4401
23	3.0803	1.5093	-2.0032	1.811	-1.2157	2.9276	-0.0249	0.1755	0.0006	-0.1851	0.0565	-0.1562	-0.0486	0.1351	-0.0045	0.1818	-0.0031	0.0053	0.1318	-0.0187	0.1613	22.8849	33.7423	-42.8655
24	2.3629	-0.0054	0.2843	1.6323	0.0417	0.5033	0.0528	0.0665	-0.0025	0.0042	-0.0065	-0.2116	-0.0521	0.0498	-0.0501	0.154	-0.0043	0.0018	0.1073	-0.0051	0.1362	24.3823	34.232	-34.1688
25	1.415	0.7251	0.121	1.8605	-0.2856	0.6965	-0.0101	-0.0623	-0.0633	0.3401	0.0435	-0.6459	0.0075	0.0798	-0.0485	0.1578	0.0009	-0.0639	0.1238	-0.0133	0.2244	33.1049	22.158	-26.9642

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 119 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 120 through 151 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 152 through 238 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 239 through 254 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 15 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 16 through 44 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 45 through 68 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 69 through 119 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 120 through 139 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 140 through 161 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 162 through 182 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 183 through 217 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 218 through 238 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 239 through 254 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 3 through 28 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 29 through 119 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 120 through 151 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 152 through 201 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 202 through 238 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 239 through 254 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 3 through 28 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 29 through 119 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 120 through 151 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 152 through 217 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 218 through 254 )

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