PDB-5t2x: Crystal structure of Uncharacterised protein lpg1670

ID or keywords:

Entry

Database: PDB / ID: 5t2x

Title

Crystal structure of Uncharacterised protein lpg1670

Components

Uncharacterized protein LPG1670

Keywords

UNKNOWN FUNCTION / Midwest Center for Structural Genomics / MCSG / PSI-Biology

Function / homology

Protein of unknown function DUF5630 / Family of unknown function (DUF5630) / Ankyrin repeat protein

Function and homology information

Biological species

Legionella pneumophila subsp. pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.303 Å

Authors

Chang, C. / Xu, X. / Cui, H. / SAVCHENKO, A. / JOACHIMIAK, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To Be Published
Title: Crystal structure of Uncharacterised protein lpg1670
Authors: Chang, C. / Xu, X. / Cui, H. / SAVCHENKO, A. / JOACHIMIAK, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Aug 24, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5t2x.cif.gz	320.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5t2x.ent.gz	263.8 KB	Display	PDB format
PDBx/mmJSON format	5t2x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5t2x_validation.pdf.gz	428.2 KB	Display	wwPDB validaton report
Full document	5t2x_full_validation.pdf.gz	428.8 KB	Display
Data in XML	5t2x_validation.xml.gz	32.1 KB	Display
Data in CIF	5t2x_validation.cif.gz	43.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t2/5t2x ftp://data.pdbj.org/pub/pdb/validation_reports/t2/5t2x	HTTPS FTP

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Related structure data

Similar structure data	5lq2-1 5c4v-1 2qpu-1 5x13-d 4lmo-2 4z9p-d 2hyv-d 5mnj-2 2qps-d 2vza-1 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 - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC108111

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein LPG1670

B: Uncharacterized protein LPG1670

C: Uncharacterized protein LPG1670

101 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein LPG1670

defined by author&software
33.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Uncharacterized protein LPG1670

defined by author&software
33.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Uncharacterized protein LPG1670

defined by author&software
33.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	138.922, 238.831, 100.495
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Uncharacterized protein LPG1670 Mass: 33647.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1670 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q5ZUX2
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 283 / 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: 4.15 Å³/Da / Density % sol: 70.38 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Bis-Tris, 3.5M Sodium formate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97952 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 20, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.97952 Å / Relative weight: 1

Reflection

Resolution: 2.28→50 Å / Num. obs: 71709 / % possible obs: 98 % / Redundancy: 9.4 % / B_iso Wilson estimate: 33.02 Å² / R_merge(I) obs: 0.102 / R_pim(I) all: 0.034 / R_rim(I) all: 0.108 / Χ²: 1.076 / Net I/av σ(I): 21.578 / Net I/σ(I): 9.5 / Num. measured all: 670803

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.28-2.32	9.1	0.792	3456	0.897	0.267	0.838	0.661	95.5
2.32-2.36	9.3	0.75	3418	0.889	0.251	0.793	0.675	94.8
2.36-2.41	9.3	0.774	3436	0.898	0.258	0.818	0.677	94.7
2.41-2.46	9.3	0.601	3419	0.926	0.2	0.635	0.703	94.8
2.46-2.51	9.3	0.521	3480	0.952	0.173	0.55	0.733	96
2.51-2.57	9.3	0.385	3498	0.964	0.128	0.407	0.775	96.9
2.57-2.63	9.3	0.365	3569	0.967	0.122	0.386	0.808	97.8
2.63-2.7	9.3	0.281	3550	0.977	0.093	0.297	0.887	98.4
2.7-2.78	9.4	0.247	3590	0.982	0.082	0.261	0.906	99.2
2.78-2.87	9.5	0.217	3621	0.986	0.072	0.228	0.994	99.3
2.87-2.98	9.7	0.187	3647	0.988	0.062	0.198	1.086	99.8
2.98-3.09	9.8	0.151	3607	0.991	0.05	0.16	1.253	99.6
3.09-3.24	9.8	0.137	3637	0.992	0.045	0.144	1.423	99.6
3.24-3.41	9.7	0.12	3640	0.994	0.04	0.126	1.595	99.7
3.41-3.62	9.5	0.104	3664	0.994	0.035	0.11	1.657	99.6
3.62-3.9	9.3	0.088	3663	0.996	0.029	0.092	1.609	99.7
3.9-4.29	9.1	0.081	3681	0.996	0.027	0.085	1.464	99.7
4.29-4.91	9.1	0.074	3687	0.996	0.025	0.078	1.346	99.7
4.91-6.19	9.2	0.072	3725	0.997	0.024	0.076	1.148	99.8
6.19-50	8.5	0.056	3721	0.997	0.02	0.059	0.894	95.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2386: ???)	refinement
PDB_EXTRACT	3.2	data extraction
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.303→27.661 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.86 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2338	3363	5.01 %
R_work	0.2102	-	-
obs	0.2114	67165	90.76 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.303→27.661 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6257	0	0	283	6540

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.001	6401
X-RAY DIFFRACTION	f_angle_d	0.412	8650
X-RAY DIFFRACTION	f_dihedral_angle_d	11.515	3812
X-RAY DIFFRACTION	f_chiral_restr	0.032	939
X-RAY DIFFRACTION	f_plane_restr	0.002	1088

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 (%)
2.3033-2.3362	0.3052	95	0.2513	1729	X-RAY DIFFRACTION	60
2.3362-2.371	0.3171	107	0.2586	2171	X-RAY DIFFRACTION	75
2.371-2.4081	0.3254	116	0.2641	2246	X-RAY DIFFRACTION	77
2.4081-2.4475	0.3051	118	0.2685	2349	X-RAY DIFFRACTION	81
2.4475-2.4897	0.3448	121	0.2693	2379	X-RAY DIFFRACTION	83
2.4897-2.5349	0.2756	132	0.2763	2431	X-RAY DIFFRACTION	84
2.5349-2.5837	0.3321	138	0.2581	2546	X-RAY DIFFRACTION	87
2.5837-2.6364	0.2962	139	0.2572	2609	X-RAY DIFFRACTION	90
2.6364-2.6936	0.2998	143	0.26	2648	X-RAY DIFFRACTION	92
2.6936-2.7562	0.2848	132	0.2568	2740	X-RAY DIFFRACTION	93
2.7562-2.8251	0.2711	149	0.2661	2695	X-RAY DIFFRACTION	93
2.8251-2.9014	0.3079	145	0.269	2775	X-RAY DIFFRACTION	95
2.9014-2.9867	0.2941	145	0.2639	2812	X-RAY DIFFRACTION	96
2.9867-3.083	0.2935	134	0.2639	2780	X-RAY DIFFRACTION	95
3.083-3.193	0.2833	183	0.2536	2767	X-RAY DIFFRACTION	96
3.193-3.3206	0.2652	142	0.2495	2849	X-RAY DIFFRACTION	97
3.3206-3.4715	0.2195	157	0.2164	2825	X-RAY DIFFRACTION	97
3.4715-3.6541	0.2556	144	0.1999	2874	X-RAY DIFFRACTION	98
3.6541-3.8825	0.2162	135	0.1765	2867	X-RAY DIFFRACTION	97
3.8825-4.1813	0.165	138	0.1671	2905	X-RAY DIFFRACTION	98
4.1813-4.6004	0.1582	170	0.1481	2907	X-RAY DIFFRACTION	99
4.6004-5.2621	0.1786	162	0.1595	2922	X-RAY DIFFRACTION	99
5.2621-6.6147	0.2233	181	0.1993	2978	X-RAY DIFFRACTION	100
6.6147-27.6634	0.1717	137	0.1794	2998	X-RAY DIFFRACTION	96

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	0.0064	0.006	-0.0005	0.006	-0.0029	0.0044	0.0011	-0.0003	0.0208	0.0316	0.0111	-0.0136	-0.0089	0.0363	0	0.3282	-0.0767	0.0838	0.3474	-0.052	0.3444	50.1528	37.1476	59.0787
2	0.018	0.0108	-0.0222	0.0333	-0.0072	0.0238	0.0037	0.0135	0.0434	0.0742	0.0303	0.0941	-0.0321	0.0493	0.0161	0.3581	-0.0777	0.1718	0.2472	-0.015	0.3649	34.435	31.7533	60.8168
3	0.0155	-0.0027	0.0014	0.0091	-0.0045	0.0052	0.0493	0.0189	0.063	-0.0231	0.0575	-0.0002	-0.0165	0.0092	0.0701	0.347	-0.061	0.094	0.2195	-0.0007	0.2119	31.5879	17.293	55.0279
4	0.0046	0.0071	-0.001	0.0827	-0.0184	0.0432	0.1004	-0.0102	0.1089	0.0215	0.0886	0.1123	-0.0966	0.0708	0.3147	0.3112	0.0351	0.312	0.1818	0.0266	0.291	21.7485	8.7198	65.0903
5	0.0084	0.0051	-0.0101	0.0076	-0.0053	0.0084	0.0551	-0.0551	0.0859	0.0343	0.0278	0.0643	-0.1001	-0.0255	0.0623	0.3512	0.0172	0.4158	0.2006	0.0675	0.5672	13.4947	15.9634	72.2226
6	0.0031	-0.0001	-0.0002	0.0014	-0.0024	0.0026	0.0028	-0.0014	0.009	-0.0086	0.0062	-0.0094	-0.0073	-0.0062	-0	0.4618	0.0208	0.1105	0.5105	0.1213	0.5427	10.4391	21.6859	60.3045
7	0.0318	0.0061	0.0011	0.0098	0.01	0.009	-0.0041	-0.0542	-0.0814	0.0876	0.0752	0.0805	-0.085	-0.0119	0.0533	0.4821	-0.0164	0.4669	0.4433	-0.045	0.5981	9.39	13.2889	78.8673
8	0.0092	-0.004	-0.0046	0.0049	-0.002	0.0039	0.0182	-0.0423	0.0375	0.0073	-0.0072	-0.0266	0.0187	0.0194	0	0.301	0.0747	-0.0262	0.4715	-0.1223	0.3639	92.0896	34.9869	42.5385
9	0.0033	-0.0007	-0.0004	0.0019	0.0006	0.0009	0.0161	-0.0216	-0.0648	-0.0054	-0.006	0.0451	0.0078	0.0063	0	0.2357	0.0057	0.041	0.4725	-0.1045	0.2914	82.1522	36.7662	43.9993
10	0.0272	0.0192	0.0036	0.0278	-0.0018	0.0236	0.0758	-0.0352	0.0854	0.0228	0.0267	-0.0203	-0.0351	0.0088	0.0149	0.2295	-0.0334	0.0701	0.4141	-0.2148	0.4622	77.5695	52.555	44.3604
11	0.0073	-0.0011	-0.0034	0.0185	-0.0063	0.0064	0.0749	0.0585	0.0271	-0.0527	0.0961	-0.0947	-0.0051	0.0742	0.0837	0.1804	0.0136	0.0414	0.3623	-0.0706	0.2069	65.556	41.0302	38.2903
12	0.0508	0.0299	-0.0196	0.0243	-0.004	0.0385	0.0795	-0.0423	0.1453	0.0223	0.0773	-0.0031	-0.0256	0.0868	0.2484	0.2163	-0.0274	0.1649	0.2223	-0.2846	0.2288	53.1059	45.26	48.2418
13	0.0166	-0.0073	-0.0144	0.0038	0.0071	0.0135	0.0333	-0.0528	0.0899	0.0309	0.0647	-0.0374	-0.0626	0.0865	0.0851	0.3162	-0.1081	0.2522	0.3401	-0.3959	0.5361	55.4407	56.1478	54.8936
14	0.0221	-0.0256	0.0219	0.0278	-0.0286	0.0561	-0.017	0.0213	0.0424	-0.0186	-0.0447	0.0491	-0.0198	0.0093	-0.1565	0.3795	0.0844	0.1953	0.3575	-0.2703	0.6143	48.8711	61.722	50.8131
15	0.021	-0.0015	0.0037	0.0158	-0.0043	0.0037	0.0427	-0.0051	-0.0061	0.0869	0.0185	0.0315	-0.0095	0.0428	0.0844	0.5218	-0.0489	0.0987	0.6079	-0.4084	0.4396	55.3343	56.3828	66.3642
16	0.0017	-0.001	-0	0.0102	0.0014	0.0025	-0.0191	-0.0522	-0.0122	0.0206	0.0285	-0.0297	0.049	-0.0024	0	0.4149	0.0294	-0.099	0.256	-0.0468	0.3744	111.5017	-2.2048	25.6577
17	0.0317	-0.0212	-0.0083	0.0296	0.0145	0.0252	0.0233	-0.0456	0.0353	-0.0207	0.0651	-0.0748	0.0738	0.0233	0.0248	0.3496	0.0897	-0.1115	0.2719	-0.1365	0.3548	114.4909	14.0881	27.5381
18	0.0181	0.0012	-0.0116	0.0113	-0.0005	0.0072	0.0614	0.0327	-0.0481	-0.0806	0.0822	-0.0548	0.0468	0.0255	0.0824	0.3148	0.0726	-0.0494	0.2412	-0.081	0.2127	103.3221	23.7467	21.7086
19	0.0835	-0.0211	-0.024	0.0513	0.041	0.1127	0.072	-0.0278	0.0557	0.0182	0.143	-0.1525	0.0832	0.0606	0.3412	0.2185	-0.0013	-0.1369	0.2713	-0.2709	0.2414	100.7103	36.5602	31.7344
20	0.0018	0.0044	0.0032	0.0204	0.0175	0.0115	0.0697	-0.0261	-0.0026	0.0814	0.04	-0.0898	0.0665	0.076	0.103	0.2566	0.0406	-0.1999	0.3813	-0.4382	0.5741	111.0912	40.0908	38.9462
21	0.0015	0.0013	-0.0017	0.0018	0.0006	0.0013	0.0063	-0.0019	0.0081	-0.0098	-0.0093	-0.0115	-0.0019	0.0187	-0	0.4907	-0.0566	0.012	0.5282	-0.1538	0.538	117.313	40.4113	27.2972
22	0.0265	0.0172	0.0193	0.0294	0.0025	0.0093	0.0547	-0.1228	0.0894	0.0139	0.0254	0.0177	0.0392	0.0835	0.0567	0.465	-0.0011	-0.2585	0.4109	-0.3796	0.5446	110.7517	44.9628	45.5667

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 40 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 90 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 91 through 131 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 132 through 186 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 187 through 220 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 221 through 236 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 237 through 274 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 14 through 40 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 41 through 62 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 63 through 90 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 91 through 131 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 132 through 186 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 187 through 221 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 222 through 251 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 252 through 274 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 14 through 40 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 41 through 90 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 91 through 131 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 132 through 186 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 187 through 220 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 221 through 236 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 237 through 274 )

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

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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

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Yorodumi