PDB-3b48: Crystal structure of unknown function protein EF1359

ID or keywords:

Entry

Database: PDB / ID: 3b48

Title

Crystal structure of unknown function protein EF1359

Components

Uncharacterized protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Enterococcus faecalis V583 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / glycerol catabolic process / membrane
Similarity search - Function

Biological species

Enterococcus faecalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.21 Å

Authors

Chang, C. / Li, H. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of unknown function protein EF1359.
Authors: Chang, C. / Li, H. / Moy, S. / Joachimiak, A.

History

Deposition	Oct 23, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3b48.cif.gz	161.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3b48.ent.gz	131.6 KB	Display	PDB format
PDBx/mmJSON format	3b48.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3b48_validation.pdf.gz	463.9 KB	Display	wwPDB validaton report
Full document	3b48_full_validation.pdf.gz	475 KB	Display
Data in XML	3b48_validation.xml.gz	36 KB	Display
Data in CIF	3b48_validation.cif.gz	48 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b4/3b48 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/3b48	HTTPS FTP

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Related structure data

Similar structure data	4ib2-1 3dnz-d 4ru1-10 6dzx-5 6dzx-1 4mwp-d 4yah-d 3l57-2 2whz-d 4ru1-6 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC29051

Similar structure data

Other databases

TargetDB: APC29051

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

E: Uncharacterized protein

F: Uncharacterized protein

88.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein

B: Uncharacterized protein

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

2

C: Uncharacterized protein

D: Uncharacterized protein

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

3

E: Uncharacterized protein

F: Uncharacterized protein

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

Unit cell

Length a, b, c (Å)	60.080, 102.112, 60.454
Angle α, β, γ (deg.)	90.00, 96.57, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Uncharacterized protein Mass: 14747.447 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_1359 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q835L8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.92 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05M MgCl2, 0.1M HEPES, 30% PEG MME550, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97917 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2005
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97917 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 36096 / Num. obs: 34382 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / B_iso Wilson estimate: 34.6 Å² / R_merge(I) obs: 0.103 / Net I/σ(I): 24.72
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.422 / Mean I/σ(I) obs: 2.73 / Num. unique all: 3012 / % possible all: 83.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.21→44.99 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.907 / SU B: 13.539 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.399 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2463	1713	5 %	RANDOM
R_work	0.20074	-	-	-
all	0.20304	32645	-	-
obs	0.20304	32645	94.55 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 30.475 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.68 Å²	0 Å²	0.1 Å²
2-	-	0.51 Å²	0 Å²
3-	-	-	2.19 Å²

Refinement step

Cycle: LAST / Resolution: 2.21→44.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5880	0	0	236	6116

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	5956
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.457	1.964	8037
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.396	5	780
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.864	27.154	253
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.235	15	1056
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.397	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	946
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4386
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	2848
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.297	0.2	4032
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.236	0.2	373
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.306	0.2	53
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.237	0.2	15
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.936	1.5	4022
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.191	2	6198
X-RAY DIFFRACTION	r_scbond_it	2.189	3	2148
X-RAY DIFFRACTION	r_scangle_it	3.161	4.5	1839
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.21→2.268 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.271	96	-
R_work	0.232	1884	-
obs	-	1980	73.83 %

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	4.5106	0.1278	1.1895	3.8235	-0.5191	2.7917	0.1895	0.1311	0.0684	-0.0563	-0.1117	-0.2649	-0.0809	0.1707	-0.0778	-0.1411	0.0055	0.0269	-0.1209	-0.0197	-0.0821	29.3678	13.5294	11.9811
2	5.1604	-0.8138	2.2345	3.308	-0.9659	4.1834	-0.1077	-0.1322	0.5702	0.2036	-0.0744	-0.0968	-0.4448	-0.1778	0.1821	-0.07	-0.0199	0.0306	-0.1019	0.01	-0.0497	25.076	21.625	14.7779
3	6.8748	1.1112	-0.9708	3.5306	0.0671	1.8706	0.0775	0.337	-0.373	-0.111	-0.0999	-0.4108	0.1566	0.0807	0.0224	-0.0475	0.0021	0.0065	-0.1123	-0.0131	-0.0314	33.2535	4.7677	11.5491
4	10.742	-4.1624	-6.9268	6.3743	6.5778	7.6507	-0.172	-0.3225	-0.0193	0.9063	0.4778	-0.1511	0.6845	0.085	-0.3058	-0.0183	0.0105	0.0061	0.0401	0.0041	-0.0276	9.4887	23.9023	23.5558
5	4.3411	-0.3327	-0.1303	2.3602	0.6946	3.3382	0.092	-0.0812	0.0115	0.0335	-0.054	0.3596	0.0643	-0.2366	-0.038	-0.1642	0.0029	-0.0172	-0.073	0.0321	-0.0735	3.0471	20.1798	11.8285
6	3.5701	-0.3283	-0.3652	4.0986	-0.0362	2.6879	-0.0532	-0.1168	-0.5664	0.0703	0.0866	0.1662	0.4464	0.1393	-0.0334	-0.089	-0.0049	-0.0536	-0.039	0.0609	-0.0397	6.755	11.2193	13.352
7	5.6225	1.4292	0.4913	3.5719	0.3471	2.9382	0.1098	-0.1327	0.289	0.117	-0.0156	0.3126	-0.153	-0.2903	-0.0942	-0.0802	0.037	-0.0111	-0.074	0.0209	0.0286	-0.968	28.8746	12.3425
8	24.2473	-21.011	-1.9478	18.6395	4.8914	23.8678	-0.8261	-0.3927	0.5682	0.4702	1.4355	-0.3235	-0.362	0.6736	-0.6094	-0.0508	0.0352	-0.0408	-0.0179	-0.0236	-0.0125	22.2295	9.1777	22.2146
9	3.2185	0.4655	-0.393	2.8802	-0.0377	1.6805	-0.0798	0.1257	0.2567	-0.1779	0.1193	-0.1868	-0.1069	0.1845	-0.0396	-0.0645	-0.0453	0.0093	-0.1062	0.0259	-0.0854	23.9422	-17.2384	10.816
10	3.4438	-0.73	-0.9876	3.1751	0.296	1.3833	-0.1397	0.0855	-0.2658	-0.1231	-0.0275	0.1695	0.09	-0.1086	0.1672	-0.0664	-0.02	-0.0162	-0.1006	0.0062	-0.0955	17.9391	-24.7475	10.0723
11	6.4814	0.0659	-2.352	3.0881	0.4478	2.9499	-0.0951	0.1873	0.345	-0.1472	0.1097	-0.3079	-0.0765	0.1342	-0.0145	-0.0314	-0.047	-0.0069	-0.0993	0.0462	0.0059	29.0322	-9.4928	9.3515
12	15.4768	-9.3292	-14.7221	6.5475	5.3478	27.4641	0.1402	1.6889	-0.2941	-0.0681	0.1407	0.8139	0.2983	-0.2902	-0.281	-0.0841	-0.0468	-0.0488	0.007	-0.0457	0.0172	-0.2502	-23.7559	8.4565
13	5.6117	-0.2697	-0.0069	2.7541	0.2759	2.4629	-0.0887	-0.3154	0.2549	0.0724	0.0786	0.3759	-0.1132	-0.2072	0.0101	-0.0985	-0.0015	0.0297	-0.1171	-0.0417	-0.0716	-1.1779	-19.1673	21.8399
14	3.2264	0.1235	-1.2596	4.3715	-1.0214	3.2392	-0.053	0.0936	0.8514	-0.0443	0.0936	0.319	-0.2284	0.0582	-0.0406	-0.0368	-0.0215	0.0041	-0.119	-0.0299	-0.0241	2.7457	-11.2937	17.717
15	6.3448	-0.866	-2.3763	1.822	0.147	4.9513	-0.0366	-0.3365	-0.421	0.1155	0.0459	0.5685	0.1968	-0.2991	-0.0093	-0.0383	-0.0264	0.047	-0.0577	0.0076	0.0051	-6.0602	-27.0076	23.7328
16	19.1594	5.4642	12.413	1.5967	3.6885	8.6157	-0.4443	0.3016	1.9602	-0.7092	1.2988	0.7171	0.6297	-0.575	-0.8545	-0.0025	-0.0451	-0.0608	-0.0403	0.18	0.0531	13.7874	-10.6732	4.6011
17	4.5847	0.8339	-0.4379	4.389	0.2364	4.1625	-0.1259	-0.0093	-0.0882	-0.1779	0.1208	0.4043	0.2566	-0.3398	0.0051	-0.097	-0.0203	-0.0744	-0.1121	0.0233	-0.1502	23.9863	2.746	38.4994
18	4.1266	2.6347	-0.8182	7.8287	-0.7392	3.3424	0.0196	0.2231	-0.7877	0.2732	0.1027	0.0293	0.4584	-0.0249	-0.1223	-0.033	0.0104	-0.0568	-0.0582	0.024	-0.0447	28.2348	-5.5979	41.6765
19	7.3024	0.9023	1.7888	2.5755	1.2858	3.7675	-0.2238	0.2796	0.6852	-0.192	0.0555	0.602	-0.1621	-0.4222	0.1683	-0.0539	-0.0057	-0.0648	-0.0204	0.0661	-0.0718	18.5196	10.242	37.1347
20	10.7203	7.127	10.6054	7.4932	2.3908	18.3728	-0.4468	-1.8213	-0.6688	0.2191	1.5663	0.267	-0.2957	-1.5454	-1.1195	-0.0508	-0.011	0.0365	0.2305	0.0786	-0.1294	38.6971	-5.6565	55.0817
21	3.6358	0.8889	1.0109	1.8756	0.2515	2.8963	0.1079	0.0495	-0.2394	0.1142	0.0388	-0.2875	0.1216	0.2268	-0.1467	-0.0824	0.0358	-0.021	-0.1455	0.0016	-0.0297	49.3791	0.6264	48.371
22	2.6049	0.0623	0.3416	3.7964	0.9582	1.1232	0.0041	-0.0286	0.1052	0.121	-0.1046	0.0349	-0.176	-0.1812	0.1005	-0.0639	-0.0144	-0.016	-0.0958	-0.0074	-0.0978	43.5031	8.1276	49.2907
23	4.9104	0.4862	0.8019	4.1969	0.6241	2.5136	0.1539	0.1118	-0.271	0.1306	-0.0027	-0.2889	0.2642	0.3104	-0.1512	-0.0685	0.0375	0.0005	-0.0832	0.0066	0.0227	54.4246	-7.3604	49.661
24	6.32	4.8197	-6.0459	7.9588	10.0333	55.8489	-0.218	0.5466	-0.1755	1.2138	-0.0918	0.8506	-0.8756	-1.6838	0.3099	-0.1176	-0.0251	0.0163	0.0161	0.0137	-0.0511	25.3815	6.2896	51.8134

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 10	4 - 13
2	X-RAY DIFFRACTION	1	A	A	29 - 44	32 - 47
3	X-RAY DIFFRACTION	1	A	A	61 - 70	64 - 73
4	X-RAY DIFFRACTION	1	A	A	90 - 98	93 - 101
5	X-RAY DIFFRACTION	2	A	A	11 - 26	14 - 29
6	X-RAY DIFFRACTION	2	A	A	99 - 126	102 - 129
7	X-RAY DIFFRACTION	3	A	A	45 - 60	48 - 63
8	X-RAY DIFFRACTION	3	A	A	71 - 89	74 - 92
9	X-RAY DIFFRACTION	4	A	A	127 - 132	130 - 135
10	X-RAY DIFFRACTION	5	B	B	1 - 10	4 - 13
11	X-RAY DIFFRACTION	5	B	B	29 - 44	32 - 47
12	X-RAY DIFFRACTION	5	B	B	61 - 70	64 - 73
13	X-RAY DIFFRACTION	5	B	B	90 - 98	93 - 101
14	X-RAY DIFFRACTION	6	B	B	11 - 28	14 - 31
15	X-RAY DIFFRACTION	6	B	B	99 - 126	102 - 129
16	X-RAY DIFFRACTION	7	B	B	45 - 60	48 - 63
17	X-RAY DIFFRACTION	7	B	B	71 - 89	74 - 92
18	X-RAY DIFFRACTION	8	B	B	127 - 132	130 - 135
19	X-RAY DIFFRACTION	9	C	C	1 - 10	4 - 13
20	X-RAY DIFFRACTION	9	C	C	29 - 44	32 - 47
21	X-RAY DIFFRACTION	9	C	C	61 - 70	64 - 73
22	X-RAY DIFFRACTION	9	C	C	90 - 98	93 - 101
23	X-RAY DIFFRACTION	10	C	C	11 - 28	14 - 31
24	X-RAY DIFFRACTION	10	C	C	99 - 126	102 - 129
25	X-RAY DIFFRACTION	11	C	C	45 - 60	48 - 63
26	X-RAY DIFFRACTION	11	C	C	71 - 89	74 - 92
27	X-RAY DIFFRACTION	12	C	C	127 - 132	130 - 135
28	X-RAY DIFFRACTION	13	D	D	1 - 10	4 - 13
29	X-RAY DIFFRACTION	13	D	D	29 - 44	32 - 47
30	X-RAY DIFFRACTION	13	D	D	61 - 70	64 - 73
31	X-RAY DIFFRACTION	13	D	D	90 - 98	93 - 101
32	X-RAY DIFFRACTION	14	D	D	11 - 26	14 - 29
33	X-RAY DIFFRACTION	14	D	D	99 - 126	102 - 129
34	X-RAY DIFFRACTION	15	D	D	45 - 59	48 - 62
35	X-RAY DIFFRACTION	15	D	D	71 - 89	74 - 92
36	X-RAY DIFFRACTION	16	D	D	127 - 131	130 - 134
37	X-RAY DIFFRACTION	17	E	E	1 - 10	4 - 13
38	X-RAY DIFFRACTION	17	E	E	29 - 44	32 - 47
39	X-RAY DIFFRACTION	17	E	E	61 - 70	64 - 73
40	X-RAY DIFFRACTION	17	E	E	90 - 98	93 - 101
41	X-RAY DIFFRACTION	18	E	E	11 - 28	14 - 31
42	X-RAY DIFFRACTION	18	E	E	99 - 126	102 - 129
43	X-RAY DIFFRACTION	19	E	E	45 - 60	48 - 63
44	X-RAY DIFFRACTION	19	E	E	71 - 89	74 - 92
45	X-RAY DIFFRACTION	20	E	E	127 - 131	130 - 134
46	X-RAY DIFFRACTION	21	F	F	1 - 10	4 - 13
47	X-RAY DIFFRACTION	21	F	F	29 - 44	32 - 47
48	X-RAY DIFFRACTION	21	F	F	61 - 70	64 - 73
49	X-RAY DIFFRACTION	21	F	F	90 - 98	93 - 101
50	X-RAY DIFFRACTION	22	F	F	11 - 28	14 - 31
51	X-RAY DIFFRACTION	22	F	F	99 - 126	102 - 129
52	X-RAY DIFFRACTION	23	F	F	45 - 60	48 - 63
53	X-RAY DIFFRACTION	23	F	F	71 - 89	74 - 92
54	X-RAY DIFFRACTION	24	F	F	127 - 132	130 - 135

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