PDB-5l0l: Crystal structure of Uncharacterized protein LPG0439

ID or keywords:

Entry

Database: PDB / ID: 5l0l

Title

Crystal structure of Uncharacterized protein LPG0439

Components

Uncharacterized protein

Keywords

UNKNOWN FUNCTION

Function / homology

: / HIT-related / membrane / LPG0439 HIT-related domain-containing protein

Function and homology information

Biological species

Legionella pneumophila subsp. pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Chang, C. / Skarina, T. / Khutoreskaya, G. / Savchenko, A. / Joachimiak, A.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Uncharacterized protein LPG0439
Authors: Chang, C. / Skarina, T. / Khutoreskaya, G. / Savchenko, A. / Joachimiak, A.

History

Deposition	Jul 27, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 10, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 17, 2016	Group: Database references / Structure summary
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Nov 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5l0l.cif.gz	196.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5l0l.ent.gz	159 KB	Display	PDB format
PDBx/mmJSON format	5l0l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l0/5l0l ftp://data.pdbj.org/pub/pdb/validation_reports/l0/5l0l	HTTPS FTP

-
Related structure data

Similar structure data	3htn-d 7d6a-1 1t0a-d 4co3-2 6cci-d 5n6s-4 4gsn-1 4co0-1 3f6m-1 6peu-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	129.688, 129.688, 117.143
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	180
Space group name H-M	P6₂22

Components on special symmetry positions

ID	Model	Components
1	1	A-504- HOH
2	1	A-628- HOH
3	1	B-621- HOH
4	1	B-651- HOH

#1: Protein	Uncharacterized protein Mass: 24698.088 Da / Num. of mol.: 2 / Fragment: residues 94-308 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0439 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q5ZYD3
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 45.95 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: % Peg2KMME, Ammonium sulfate 0.2M, 0.1M sodium acetate

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97929 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2012

Radiation

Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97929 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. obs: 54185 / % possible obs: 99.9 % / Redundancy: 11.6 % / R_merge(I) obs: 0.125 / Χ²: 2.421 / Net I/av σ(I): 34 / Net I/σ(I): 7.9 / Num. measured all: 630221

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
1.8-1.82	9.4	0.907	1312	0.821	100
1.82-1.83	9.9	0.897	1334	0.818	100
1.83-1.85	10.7	0.876	1338	0.831	100
1.85-1.86	11.4	0.875	1322	0.85	100
1.86-1.88	11.5	0.768	1332	0.88	100
1.88-1.9	11.7	0.703	1332	0.879	100
1.9-1.92	11.6	0.636	1340	0.907	100
1.92-1.94	11.6	0.564	1323	0.95	100
1.94-1.96	11.8	0.534	1340	0.948	100
1.96-1.98	11.7	0.457	1323	1.02	100
1.98-2	11.7	0.425	1339	1.037	100
2-2.03	11.7	0.378	1360	1.081	100
2.03-2.05	11.8	0.369	1312	1.109	100
2.05-2.08	11.8	0.331	1345	1.215	100
2.08-2.11	11.9	0.311	1333	1.213	100
2.11-2.13	11.8	0.286	1346	1.253	100
2.13-2.16	11.8	0.264	1337	1.301	100
2.16-2.2	11.8	0.249	1336	1.362	100
2.2-2.23	11.9	0.228	1334	1.409	100
2.23-2.27	11.9	0.209	1346	1.501	100
2.27-2.31	11.9	0.202	1346	1.501	100
2.31-2.35	11.9	0.187	1360	1.595	100
2.35-2.39	12	0.179	1337	1.647	100
2.39-2.44	12.1	0.172	1341	1.757	100
2.44-2.5	12	0.158	1367	1.843	100
2.5-2.55	12.2	0.158	1332	1.94	100
2.55-2.62	12.1	0.139	1346	2.187	100
2.62-2.69	12.1	0.136	1356	2.267	100
2.69-2.77	12	0.129	1360	2.562	100
2.77-2.86	12.1	0.119	1365	2.649	100
2.86-2.96	12	0.107	1361	3.11	100
2.96-3.08	12	0.104	1363	3.499	100
3.08-3.22	11.9	0.102	1355	4.233	100
3.22-3.39	11.8	0.095	1384	4.627	100
3.39-3.6	11.6	0.085	1379	4.953	99.9
3.6-3.88	11.6	0.079	1384	5.117	100
3.88-4.27	11.5	0.077	1393	5.664	100
4.27-4.88	11.3	0.066	1416	5.237	100
4.88-6.15	11.4	0.083	1435	7.831	100
6.15-50	10.6	0.078	1521	9.701	98.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.2	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→50.01 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.952 / SU B: 3.815 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.095
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1889	2752	5.1 %	RANDOM
R_work	0.169	-	-	-
obs	0.17	51384	99.92 %	-

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 max: 84.93 Å² / B_iso mean: 26.755 Å² / B_iso min: 11.36 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.77 Å²	-0.38 Å²	-0 Å²
2-	-	-0.77 Å²	-0 Å²
3-	-	-	2.5 Å²

Refinement step

Cycle: final / Resolution: 1.8→50.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3426	0	11	326	3763
B_iso mean	-	-	22.52	30.43	-
Num. residues	-	-	-	-	430

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	3651
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3425
X-RAY DIFFRACTION	r_angle_refined_deg	1.529	1.972	4956
X-RAY DIFFRACTION	r_angle_other_deg	0.917	3	7923
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.861	5	455
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.967	24.438	169
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.989	15	601
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.712	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	533
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	4168
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	838
X-RAY DIFFRACTION	r_mcbond_it	1.021	1.292	1793
X-RAY DIFFRACTION	r_mcbond_other	1.021	1.291	1792
X-RAY DIFFRACTION	r_mcangle_it	1.824	1.923	2257

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.256	222	-
R_work	0.235	3695	-
all	-	3917	-
obs	-	-	99.97 %

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	10.3838	10.5863	-1.2301	12.6487	-2.6286	1.9274	-0.204	0.6694	-0.268	-0.273	0.0349	-0.2454	0.0842	0.2994	0.1691	0.1279	-0.0156	0.0249	0.2861	-0.0515	0.0433	90.3575	28.7716	-14.2413
2	11.1163	8.7286	2.5308	6.8768	2.1727	2.7783	-0.4372	0.2735	0.364	-0.358	0.2289	0.2805	0.0165	0.2864	0.2083	0.1838	-0.0556	0.0432	0.136	-0.0097	0.0988	98.2937	40.3179	-4.4535
3	1.9027	-1.5561	-0.7886	5.9304	1.4571	0.5969	0.0445	0.2077	-0.0944	-0.1566	0.0022	-0.3908	-0.1327	0.0661	-0.0467	0.1054	-0.0461	0.0122	0.2045	-0.0651	0.1828	103.7678	32.3403	4.835
4	1.5365	-0.4	-0.6633	1.438	0.8546	0.6395	-0.0181	0.1609	-0.0562	-0.0418	0.0515	-0.0977	-0.0401	-0.0249	-0.0334	0.1293	-0.0105	0.0069	0.1598	-0.0431	0.1276	94.9544	35.2476	6.1104
5	10.9101	-3.6245	10.8768	3.5397	-1.6757	12.5841	-0.2098	0.5431	0.4513	0.0972	-0.0631	-0.591	-0.1266	0.5304	0.2729	0.0615	-0.0439	0.0986	0.182	-0.0959	0.3378	106.1294	28.9357	-5.9417
6	0.4487	0.3368	0.3372	0.7232	0.1856	0.9379	-0.0219	0.047	-0.1055	0.0087	0.0822	-0.1429	-0.0225	-0.0026	-0.0603	0.1164	-0.0162	0.0013	0.1281	-0.0529	0.1343	92.8432	27.2385	5.6942
7	7.7656	4.713	3.5512	4.2298	1.4726	2.0507	-0.0288	0.1519	0.1727	-0.1732	0.0175	0.1192	0.0285	0.0393	0.0113	0.1656	-0.0401	0.0236	0.2061	-0.0095	0.0698	82.7769	29.575	-12.2795
8	0.5529	0.3615	-0.2358	0.6707	0.3153	0.6444	-0.0054	0.0292	-0.008	0.0605	-0.0052	0.0296	0.0088	-0.0196	0.0105	0.1367	-0.0097	-0.0045	0.1361	-0.033	0.1211	85.5221	36.9495	14.4172
9	10.2139	-1.6062	-0.4638	1.6905	2.2659	3.3721	-0	-0.0078	0.0308	-0.1951	-0.1044	0.0644	-0.2932	-0.1323	0.1044	0.1326	0.0111	-0.0357	0.1361	-0.0075	0.1147	75.4495	36.6248	-1.4716
10	8.6324	4.7659	2.634	3.6213	2.2997	1.5317	-0.1449	0.243	0.2684	-0.229	0.004	0.2246	-0.168	-0.0071	0.141	0.1223	0.0137	-0.0319	0.1497	0.0006	0.1267	81.8234	44.8898	8.4591
11	1.7514	-1.7844	0.2853	3.1172	0.1822	0.2603	0.0781	-0.0229	-0.0492	0.1325	0.0058	-0.1356	0.0256	-0.0069	-0.0839	0.1428	-0.0186	-0.0501	0.1154	-0.0092	0.1662	102.3311	35.5056	18.0325
12	0.6776	0.0641	-0.4007	12.7182	-1.048	0.8042	0.1073	-0.016	0.0185	-0.1805	-0.1169	-0.4652	-0.0067	0.192	0.0096	0.0813	-0.0026	-0.0119	0.1268	-0.0182	0.1503	107.8943	33.5973	10.2213
13	1.3498	-3.2053	-0.2882	15.8511	-5.8687	5.2845	-0.1597	-0.0986	0.1597	0.7081	-0.0692	-0.7216	-0.2005	0.2345	0.2289	0.1558	-0.0365	-0.0673	0.1266	-0.0211	0.1074	85.3557	31.6399	30.2495
14	7.4525	10.0742	3.0777	23.7287	2.2508	3.3289	-0.2207	-0.3624	-0.2353	0.6407	-0.0053	0.1377	0.1414	-0.0462	0.2259	0.2315	0.0379	0.1442	0.1719	0.0869	0.127	77.9185	16.5831	32.4427
15	3.2239	4.7075	2.7502	9.7263	7.4919	6.583	0.579	0.0135	0.1853	0.417	-0.4721	0.0272	-0.0067	-0.6136	-0.1068	0.2724	-0.0057	0.0619	0.1459	0.0346	0.3024	76.0135	8.6297	21.2488
16	1.1428	0.0407	0.8304	1.2061	-0.115	0.7521	0.0018	0.0402	-0.1316	0.1652	0.0446	-0.1231	0.0051	-0.0564	-0.0464	0.1424	0.0039	-0.0352	0.0904	-0.0355	0.1687	84.6447	11.8051	12.4874
17	8.3917	-4.1388	-4.4717	5.0758	4.2517	7.03	-0.2325	0.0537	-0.554	0.3135	0.0451	0.0441	0.2325	0.0805	0.1874	0.1909	0.0025	-0.051	0.0479	0.0448	0.132	90.0304	8.5279	26.3467
18	0.261	0.4198	0.1535	0.897	0.5617	0.6904	0.0542	0.0479	-0.1258	0.0773	0.0261	-0.1376	0.01	-0.0035	-0.0803	0.1293	-0.0047	-0.0219	0.1084	-0.0356	0.1532	87.6257	19.2119	12.2512
19	0.845	-0.8336	0.0518	11.2478	1.7936	0.3343	0.0112	-0.1683	-0.0902	0.3473	-0.013	0.28	0.0676	-0.0356	0.0018	0.1863	-0.0276	0.0288	0.1321	-0.0081	0.1021	77.2739	29.0257	27.8254
20	0.3285	0.481	0.1741	0.7913	0.1349	1.0195	-0.0619	0.075	-0.034	-0.0158	0.0614	0.0144	-0.0488	-0.0085	0.0006	0.1354	-0.0167	-0.002	0.1287	-0.0534	0.1477	77.0657	20.1572	1.3807
21	11.5341	-8.0219	4.4786	18.2438	-7.1663	10.6348	0.1483	-0.2112	0.1361	-0.2378	-0.3851	0.422	0.1338	-0.1453	0.2368	0.0547	-0.0034	0.0062	0.1002	-0.0777	0.1356	69.5678	30.9487	15.4212
22	3.2	0.5645	1.2669	12.1332	2.4336	0.9105	-0.3004	0.0649	0.1399	0.1743	0.0982	0.9798	-0.0621	0.0364	0.2021	0.1275	0.0054	-0.0004	0.1094	0.0131	0.2462	66.7711	24.2795	6.413
23	3.776	-0.5643	0.6782	1.3033	0.4075	0.3384	0.033	0.0851	-0.1238	-0.0609	0.0797	-0.1835	-0.0168	0.0372	-0.1127	0.0927	-0.007	0.011	0.1031	-0.0642	0.2235	85.3173	6.1351	1.7281
24	8.5239	5.3611	1.0364	3.7537	0.3345	0.8762	-0.0343	-0.2424	-0.1703	-0.037	0.0147	-0.1184	0.1142	0.0097	0.0196	0.1033	0.0287	-0.0137	0.1521	-0.0187	0.1566	89.2385	2.3613	10.4452

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	94 - 105
2	X-RAY DIFFRACTION	2	A	106 - 113
3	X-RAY DIFFRACTION	3	A	114 - 127
4	X-RAY DIFFRACTION	4	A	128 - 149
5	X-RAY DIFFRACTION	5	A	150 - 156
6	X-RAY DIFFRACTION	6	A	157 - 203
7	X-RAY DIFFRACTION	7	A	204 - 217
8	X-RAY DIFFRACTION	8	A	218 - 252
9	X-RAY DIFFRACTION	9	A	253 - 258
10	X-RAY DIFFRACTION	10	A	259 - 269
11	X-RAY DIFFRACTION	11	A	270 - 296
12	X-RAY DIFFRACTION	12	A	297 - 308
13	X-RAY DIFFRACTION	13	B	94 - 98
14	X-RAY DIFFRACTION	14	B	99 - 105
15	X-RAY DIFFRACTION	15	B	106 - 115
16	X-RAY DIFFRACTION	16	B	116 - 149
17	X-RAY DIFFRACTION	17	B	150 - 156
18	X-RAY DIFFRACTION	18	B	157 - 202
19	X-RAY DIFFRACTION	19	B	203 - 218
20	X-RAY DIFFRACTION	20	B	219 - 253
21	X-RAY DIFFRACTION	21	B	254 - 258
22	X-RAY DIFFRACTION	22	B	259 - 266
23	X-RAY DIFFRACTION	23	B	267 - 297
24	X-RAY DIFFRACTION	24	B	298 - 308

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi