PDB-5t10: PelC dodecamer from Paraburkholderia phytofirmans, space group P6

ID or keywords:

Entry

Database: PDB / ID: 5t10

Title

PelC dodecamer from Paraburkholderia phytofirmans, space group P6

Components

Uncharacterized protein

Keywords

STRUCTURAL PROTEIN / lipoprotein / periplasmic

Function / homology

Penicillin-binding protein activator LpoB / Peptidoglycan-synthase activator LpoB / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein

Function and homology information

Biological species

Paraburkholderia phytofirmans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4987 Å

Authors

Marmont, L.S. / Howell, P.L.

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Oligomeric lipoprotein PelC guides Pel polysaccharide export across the outer membrane of Pseudomonas aeruginosa.
Authors: Marmont, L.S. / Rich, J.D. / Whitney, J.C. / Whitfield, G.B. / Almblad, H. / Robinson, H. / Parsek, M.R. / Harrison, J.J. / Howell, P.L.

History

Deposition	Aug 17, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 29, 2017	Group: Database references
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5t10.cif.gz	213.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5t10.ent.gz	173.8 KB	Display	PDB format
PDBx/mmJSON format	5t10.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/t1/5t10 ftp://data.pdbj.org/pub/pdb/validation_reports/t1/5t10	HTTPS FTP

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Related structure data

Related structure data	5t0zC 5t11SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5t11-d 1ny6-2 6umx-d 4hyy-2 2fb5-2 22167 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

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

1

A: Uncharacterized protein

B: Uncharacterized protein

A: Uncharacterized protein

B: Uncharacterized protein

A: Uncharacterized protein

B: Uncharacterized protein

A: Uncharacterized protein

B: Uncharacterized protein

A: Uncharacterized protein

B: Uncharacterized protein

A: Uncharacterized protein

B: Uncharacterized protein

defined by author
202 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_765	-y+2,x-y+1,z	1
crystal symmetry operation	3_675	-x+y+1,-x+2,z	1
crystal symmetry operation	4_775	-x+2,-y+2,z	1
crystal symmetry operation	5_565	y,-x+y+1,z	1
crystal symmetry operation	6_655	x-y+1,x,z	1

2

C: Uncharacterized protein

D: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

defined by author
202 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_765	-y+2,x-y+1,z	1
crystal symmetry operation	3_675	-x+y+1,-x+2,z	1
crystal symmetry operation	4_775	-x+2,-y+2,z	1
crystal symmetry operation	5_565	y,-x+y+1,z	1
crystal symmetry operation	6_655	x-y+1,x,z	1

Unit cell

Length a, b, c (Å)	118.113, 118.113, 85.688
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	168
Space group name H-M	P6

#1: Protein	Uncharacterized protein Mass: 16805.547 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paraburkholderia phytofirmans (bacteria) Strain: DSM 17436 / LMG 22146 / PsJN / Gene: Bphyt_1493 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2T2U6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.88 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1 M NaH2PO4/KHPO4 pH 5.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 2.499→50 Å / Num. obs: 23687 / % possible obs: 98 % / Redundancy: 21.1 % / R_merge(I) obs: 0.11 / Net I/σ(I): 28.5
Reflection shell	Resolution: 2.499→2.59 Å / Redundancy: 15.8 % / R_merge(I) obs: 0.759 / % possible all: 87.2

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Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1168	refinement
DENZO		data reduction
SCALEPACK		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5T11

5t11

Resolution: 2.4987→48.626 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.12

	R_factor	Num. reflection	% reflection
R_free	0.2355	1933	8.6 %
R_work	0.185	-	-
obs	0.1895	22479	94.84 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.4987→48.626 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3878	0	0	78	3956

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3937
X-RAY DIFFRACTION	f_angle_d	1.058	5386
X-RAY DIFFRACTION	f_dihedral_angle_d	12.562	1314
X-RAY DIFFRACTION	f_chiral_restr	0.067	659
X-RAY DIFFRACTION	f_plane_restr	0.005	691

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 (%)
2.4987-2.5612	0.3524	113	0.284	1215	X-RAY DIFFRACTION	78
2.5612-2.6304	0.3171	128	0.255	1273	X-RAY DIFFRACTION	84
2.6304-2.7078	0.2947	123	0.2543	1377	X-RAY DIFFRACTION	90
2.7078-2.7952	0.3199	145	0.2189	1434	X-RAY DIFFRACTION	93
2.7952-2.8951	0.2749	134	0.213	1462	X-RAY DIFFRACTION	95
2.8951-3.011	0.2867	132	0.2225	1477	X-RAY DIFFRACTION	97
3.011-3.148	0.2867	146	0.222	1480	X-RAY DIFFRACTION	96
3.148-3.314	0.2812	140	0.2031	1525	X-RAY DIFFRACTION	98
3.314-3.5215	0.2098	142	0.1829	1524	X-RAY DIFFRACTION	99
3.5215-3.7933	0.2278	146	0.1703	1526	X-RAY DIFFRACTION	99
3.7933-4.1749	0.2186	144	0.1496	1558	X-RAY DIFFRACTION	100
4.1749-4.7785	0.1961	143	0.1344	1542	X-RAY DIFFRACTION	100
4.7785-6.0187	0.2222	151	0.1693	1559	X-RAY DIFFRACTION	100
6.0187-48.6355	0.2011	146	0.1948	1594	X-RAY DIFFRACTION	99

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	0.7576	1.7856	0.142	5.9891	2.3551	2.9257	0.3845	-0.1958	0.7865	0.3305	-0.5193	0.6679	-0.0944	-0.3051	0.1916	0.5908	0.0484	-0.1422	0.3584	-0.0769	1.2015	60.7101	153.8096	-5.7956
2	3.409	0.0168	1.4863	3.0592	0.1756	2.5515	-0.0003	-0.3565	0.0486	0.0295	-0.2876	-0.3772	0.02	0.0216	0.3074	0.2816	0.0186	0.0315	0.2922	-0.0517	0.6104	65.6394	141.2681	0.5334
3	2.3278	1.4343	1.476	6.0099	-3.3631	4.5019	0.5978	-1.1601	0.2812	2.7535	-1.0385	-0.0798	1.0397	0.4548	-0.2741	1.4934	0.0646	-0.2576	0.8095	-0.2536	0.6894	65.5446	152.3603	12.0734
4	4.1546	-0.1712	-0.0493	0.9656	-1.203	2.9328	0.4523	0.137	-0.1691	0.2067	-0.911	0.1549	0.5051	-0.9049	0.2118	0.2873	0.0502	0.0359	0.2868	-0.1015	0.5687	59.6442	132.6892	-7.6393
5	2.4133	2.3262	2.9362	8.3335	5.871	6.0122	-0.3348	-0.2944	0.095	0.2414	-0.3812	1.0105	0.1299	-0.7472	0.4719	0.296	-0.0707	0.0394	0.3836	0.0962	0.6337	57.5855	142.9142	-3.5638
6	4.4075	2.5846	1.2811	3.5406	-1.4574	3.9981	0.4673	0.5521	0.7277	-0.4114	-0.2272	-0.4134	-0.5312	-0.3197	-0.1897	0.1903	-0.0015	-0.0382	0.426	-0.0053	0.8468	57.7242	143.8293	-6.7422
7	1.3172	1.0173	0.8561	6.9599	3.2154	4.545	0.0127	0.522	0.4061	-0.8744	0.4345	-1.5611	-0.4195	0.2989	-0.3952	0.3223	-0.0247	0.0252	0.3358	0.0316	0.7062	64.2285	143.794	-10.5069
8	7.4505	-0.577	3.3812	2.7144	2.4526	3.9554	0.2143	0.1363	0.4121	-0.6507	0.0543	-0.8532	-0.0705	0.1626	-0.3883	0.7249	-0.0728	-0.1416	0.4173	-0.0319	1.0722	85.2588	145.1273	-6.5138
9	4.2014	1.349	-0.1833	4.5827	1.2883	2.1402	-0.1273	-0.6428	-0.4829	0.2692	-0.138	-0.9136	-0.0047	0.0817	0.2672	0.4055	0.0086	-0.012	0.3148	-0.0124	0.6583	84.2629	132.733	1.4101
10	3.7131	0.6477	0.1293	8.8755	1.8733	4.224	-0.0095	-0.2226	0.4845	0.6357	-0.1842	0.0577	0.0356	-0.1875	0.2762	0.3401	0.0415	0.03	0.3275	-0.0165	0.7082	78.8812	136.6564	-1.9332
11	6.5681	1.8055	0.1325	1.8747	-2.4327	4.1982	0.2711	0.5236	-0.4232	-0.7557	-0.0208	-1.6104	0.0041	0.3883	-0.3089	0.2935	0.0275	0.0427	0.366	0.0161	0.443	83.9206	134.1852	-12.1857
12	5.4097	-2.2352	0.8295	6.1659	-3.2762	1.3593	0.2159	0.0744	0.4908	0.2251	-0.426	0.1809	-0.1633	0.0987	0.1213	0.413	-0.0421	-0.0307	0.4462	-0.0221	0.4865	45.4849	141.5594	-45.6114
13	4.4244	0.7629	-3.8943	5.2103	0.3311	5.5687	0.0916	0.4807	1.4009	-0.5031	0.4089	0.6211	-0.7574	-0.0982	0.256	0.7081	0.1408	0.0096	0.4647	-0.0725	0.7085	37.8639	145.3857	-51.9413
14	5.0027	-3.0545	0.7114	3.8495	-1.4886	3.6618	0.1314	1.6021	0.1209	-0.5534	-1.0084	-0.2365	0.2537	0.9755	0.0322	0.7708	-0.0269	-0.2183	1.1248	-0.0356	0.4109	42.472	150.0451	-60.0185
15	5.3518	0.5711	0.8984	9.2183	-3.3386	7.0104	0.4919	-0.1484	-0.1409	0.5419	-0.9901	-0.3846	0.5608	0.905	0.3608	0.4459	0.0422	0.0613	0.373	-0.0691	0.2373	51.3635	131.6964	-40.5996
16	5.1219	1.8027	-0.4321	3.3343	-1.7331	2.6637	0.3386	0.1734	0.3759	-0.1089	-0.5274	-0.1267	-0.1242	0.6274	0.1675	0.5342	0.0126	-0.0618	0.3977	-0.06	0.6077	51.4159	145.4612	-45.0649
17	3.9043	-0.7197	0.2173	6.2238	-6.4499	7.9304	0.5578	-3.3528	-0.3529	2.6382	-0.1684	-0.3671	-1.1199	-1.877	-0.3394	0.8565	-0.2544	-0.2172	1.1928	0.0877	0.8028	46.865	125.9842	-28.0813
18	1.1497	0.2718	0.8202	1.4881	-1.5678	2.5722	-0.1245	-0.4189	-0.0516	0.9843	0.5252	0.217	-0.0959	-0.5425	-0.2333	0.4321	0.0509	0.0237	0.4845	-0.1677	0.2678	43.927	141.9613	-37.6598
19	4.2474	-0.8291	2.3286	5.7701	-3.9189	3.6258	-0.3	0.116	1.2078	0.0916	-0.3348	-0.721	-0.895	0.3724	0.6491	0.6312	-0.0898	-0.0381	0.5431	0.0815	0.8146	70.4031	148.0426	-44.891
20	2.4754	-0.3022	-0.4469	4.2918	-0.2844	0.5955	0.1997	0.3679	0.0521	-0.3649	-0.4624	0.5022	0.1958	-0.0546	0.0902	0.43	0.0216	-0.0668	0.403	-0.0207	0.3389	63.028	138.4394	-46.6094
21	5.0524	-2.5153	-4.0609	5.6692	3.9337	9.4982	0.0234	1.0543	1.1001	-0.5393	0.2997	0.163	-0.4104	-1.3529	-0.0399	0.425	-0.032	0.0573	0.4464	0.0034	0.4827	62.6814	149.4846	-53.2851
22	2.1274	0.7054	0.4484	0.587	0.2121	0.1023	0.21	1.3103	-0.2542	-1.5064	-0.2378	0.2123	0.5494	-1.1813	-0.0193	1.1886	0.073	-0.3243	1.0096	0.1081	0.3942	68.0495	151.3795	-60.7659
23	6.754	3.7955	-4.0832	3.6815	-1.0156	3.976	0.2124	-0.6941	-0.1296	0.2696	-0.5518	0.4043	0.3625	0.8373	0.3942	0.4967	-0.0225	-0.0655	0.4621	0.0506	0.453	67.1289	131.6271	-40.5839
24	6.606	0.1472	-0.7909	3.9724	-1.3299	3.417	0.2886	0.5038	0.4062	-0.3092	0.1885	-0.1542	0.136	0.0203	-0.0162	0.4175	-0.088	-0.014	0.4409	-0.028	0.6825	71.9071	140.8435	-44.4619
25	4.2412	-0.942	2.5663	2.3626	0.231	4.2391	0.1969	-0.1363	0.2028	0.7649	-0.4275	-0.4396	-0.5878	-0.0476	0.079	0.5359	-0.0006	-0.0564	0.4479	-0.1226	0.3985	68.7552	142.6095	-39.2676

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 20 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 81 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 82 through 89 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 90 through 108 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 109 through 119 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 120 through 140 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 141 through 158 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 4 through 20 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 21 through 79 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 80 through 134 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 135 through 160 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 4 through 49 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 50 through 78 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 79 through 89 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 90 through 108 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 109 through 134 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 135 through 140 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 141 through 159 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 4 through 28 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 29 through 50 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 51 through 79 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 80 through 89 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 90 through 108 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 109 through 119 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 120 through 159 )

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