PDB-3l48: Crystal structure of the C-terminal domain of the PapC usher

ID or keywords:

Entry

Database: PDB / ID: 3l48

Title

Crystal structure of the C-terminal domain of the PapC usher

Components

Outer membrane usher protein PapC

Keywords

TRANSPORT PROTEIN / Ig fold / greek key / Cell outer membrane /

Fimbrium /

Membrane /

Transmembrane / Transport

Function / homology

Function and homology information

fimbrial usher porin activity /

pilus assembly / cell outer membrane / membrane => GO:0016020
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Ford, B.A. / Hultgren, S.J.

Citation

Journal: J.Bacteriol. / Year: 2010
Title: Structural Homology between the C-Terminal Domain of the PapC Usher and Its Plug.
Authors: Ford, B. / Rego, A.T. / Ragan, T.J. / Pinkner, J. / Dodson, K. / Driscoll, P.C. / Hultgren, S. / Waksman, G.

History

Deposition	Dec 18, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 2, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3l48.cif.gz	167.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3l48.ent.gz	143 KB	Display	PDB format
PDBx/mmJSON format	3l48.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/l4/3l48 ftp://data.pdbj.org/pub/pdb/validation_reports/l4/3l48	HTTPS FTP

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Related structure data

Related structure data	2kt6C C: citing same article (ref.)
Similar structure data	3ph2-d 3ihs-2 5go8-2 2k94-d 3b2f-2 1igv-d 1l0s-1 4z89-5 2bzt-d 5nlj-3 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) 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

Related structure data

2kt6C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: Outer membrane usher protein PapC

B: Outer membrane usher protein PapC

C: Outer membrane usher protein PapC

D: Outer membrane usher protein PapC

E: Outer membrane usher protein PapC

hetero molecules

51.4 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Outer membrane usher protein PapC

hetero molecules

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

2

B: Outer membrane usher protein PapC

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

3

C: Outer membrane usher protein PapC

hetero molecules

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

4

D: Outer membrane usher protein PapC

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

5

E: Outer membrane usher protein PapC

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

Unit cell

Length a, b, c (Å)	100.936, 100.936, 89.540
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

#1: Protein	Outer membrane usher protein PapC Mass: 10263.684 Da / Num. of mol.: 5 / Fragment: UNP residues 749-836 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / Gene: papC, UTI89_C4893 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q1R2W8
#2: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.22 Å³/Da / Density % sol: 44.64 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% Tacsimate pH 8.0, Cryoprotected in 60% Tacsimate and 10% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
Detector	Type: NOIR-1 / Detector: CCD / Date: Feb 19, 2009
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→45.14 Å / Num. all: 27641 / Num. obs: 27641 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.4 % / B_iso Wilson estimate: 24.9 Å² / Net I/σ(I): 12.8

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: dev_241)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→45.14 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2299	2592	5.03 %	random
R_work	0.1995	-	-	-
obs	0.2011	27641	99.87 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.207 Å² / k_sol: 0.362 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.1→45.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3094	0	2	247	3343

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3180
X-RAY DIFFRACTION	f_angle_d	0.754	4352
X-RAY DIFFRACTION	f_dihedral_angle_d	15.219	1161
X-RAY DIFFRACTION	f_chiral_restr	0.05	501
X-RAY DIFFRACTION	f_plane_restr	0.002	584

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 (%)
2.1-2.1751	0.3351	256	0.2833	4865	X-RAY DIFFRACTION	100
2.1751-2.2622	0.3596	244	0.3418	4894	X-RAY DIFFRACTION	99
2.2622-2.3651	0.3079	241	0.2259	4915	X-RAY DIFFRACTION	100
2.3651-2.4898	0.2588	254	0.2043	4917	X-RAY DIFFRACTION	100
2.4898-2.6458	0.2533	270	0.2149	4888	X-RAY DIFFRACTION	100
2.6458-2.85	0.2424	293	0.2118	4847	X-RAY DIFFRACTION	100
2.85-3.1368	0.2304	307	0.1882	4865	X-RAY DIFFRACTION	100
3.1368-3.5905	0.2072	270	0.1743	4890	X-RAY DIFFRACTION	100
3.5905-4.523	0.1662	239	0.1467	4900	X-RAY DIFFRACTION	100
4.523-45.1504	0.1756	218	0.1785	4950	X-RAY DIFFRACTION	100

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	0.9926	0.522	0.0818	0.5602	-0.3382	0.3671	-0.17	0.0751	-0.0295	-0.1497	0.0957	0.1749	0.2144	-0.075	0.08	0.2019	-0.0172	-0.0441	0.0294	0.0135	0.0469	20.5356	-5.2678	-32.0752
2	0.6518	0.5548	0.1982	2.954	-0.7503	0.4821	0.0167	-0.0448	0.0485	-0.6403	-0.0046	0.0201	0.1265	-0.0037	-0.1791	0.2664	-0.0466	-0.0726	0.0654	0.0071	0.081	20.6396	-2.6207	-34.1961
3	0.578	0.2895	-0.0639	1.4977	-0.4475	1.3329	0.1123	0.0363	0.088	0.1792	0.069	0.2699	0.1834	-0.0943	-0.1746	0.1622	-0.032	-0.0528	0.0569	0.0291	0.14	15.8566	-3.8157	-30.147
4	2.6142	1.8646	2.2561	1.3207	1.5733	1.9699	-0.1878	0.0987	0.12	-0.4554	0.0922	0.2356	0.7151	-0.1566	0.0554	0.3758	-0.1322	-0.0489	0.1656	-0.0036	0.2236	14.5853	-11.4757	-30.5189
5	1.3602	0.3891	0.3497	0.153	0.265	1.224	0.0681	-0.0463	0.2011	0.2378	0.0516	-0.275	-0.1758	-0.0388	-0.0849	0.2011	-0.027	-0.0149	0.0071	-0.006	0.1231	32.9474	11.2755	-20.5364
6	0.6001	-0.7582	0.144	1.1003	0.0453	0.6203	0.0554	0.0488	0.0608	0.1622	0.0471	-0.5378	0.1112	0.1405	-0.0881	0.2581	-0.0166	-0.1172	0.0854	-0.0132	0.2731	39.5186	8.415	-17.6608
7	1.0008	0.0746	-0.3151	0.9291	0.2326	0.6647	0.0715	-0.1373	0.254	0.6395	-0.1346	0.2707	0.3386	-0.1006	0.0417	0.4196	-0.0199	-0.0534	0.0571	-0.021	0.1171	31.0261	5.3373	-12.3402
8	0.614	1.2136	-0.1748	2.6328	-0.1869	0.3129	0.1429	0.0305	0.1091	0.7761	-0.1388	-0.0228	-0.0217	0.1819	-0.0103	0.3142	0.0169	-0.0388	0.1008	0.0034	0.1324	32.1671	15.03	-13.9834
9	9.3022	-1.5508	-1.3234	8.4171	4.0337	1.9719	0.5496	1.5989	0.5017	0.5872	-0.3447	-0.0469	0.606	-0.5174	-0.2309	0.3183	0.1634	0.0163	0.4554	0.055	0.312	27.9336	18.253	-53.5459
10	2.4615	0.8479	0.1571	1.2742	-0.3221	2.8867	0.0278	0.0075	-0.1335	-0.7669	0.3704	-0.3848	-0.2024	0.1845	-0.3418	0.4148	-0.0274	0.1274	0.0978	-0.0235	0.2097	36.7614	3.6949	-39.888
11	0.6156	-0.4119	-0.6005	2.0902	0.4055	1.6807	-0.1565	0.0055	0.1287	-0.3768	0.2949	-0.5469	-0.4584	0.3184	-0.2718	0.5142	-0.0813	0.1156	0.2149	-0.0173	0.3034	37.5919	9.8422	-40.1532
12	1.3188	-0.175	-0.6043	1.6757	0.264	1.0528	-0.0024	0.0834	0.2333	-0.7979	0.2726	-0.0323	-0.3454	-0.0281	-0.1216	0.4598	-0.0976	0.0113	0.1013	0.0132	0.1147	31.8777	3.4398	-43.5915
13	0.7221	0.0822	-0.6157	0.1158	0.0788	0.8827	-0.0206	-0.0231	-0.1814	-0.747	-0.0161	-0.0337	-0.1109	0.1864	-0.0832	0.4886	-0.0612	0.0361	0.1995	0.0143	0.2146	32.6973	-2.5956	-39.6272
14	0.9947	0.3395	0.2576	0.7893	0.07	0.8399	-0.0558	-0.0308	0.0983	1.019	-0.1484	0.2883	-0.0119	-0.0392	0.1249	0.4679	-0.043	0.0892	0.0364	-0.0246	0.1019	21.0426	-15.2973	-12.0927
15	2.0233	1.2965	-0.8702	5.2261	-1.6988	0.751	-0.2646	0.2357	-0.4602	1.2289	0.0974	-0.9097	0.3121	0.135	0.3413	0.5965	-0.0171	-0.051	0.0067	0.0462	0.0605	24.8403	-19.2193	-10.9332
16	0.4389	-0.7323	0.3471	2.4534	-2.0065	2.0889	-0.0368	-0.0522	-0.1461	1.0984	-0.0674	0.874	-0.2343	-0.0777	0.0828	0.4551	-0.0259	0.2278	0.0544	-0.0407	0.2643	15.9296	-16.0153	-12.2634
17	0.3851	0.2304	0.2817	0.1516	0.0713	0.7976	-0.0304	-0.1152	0.3653	-0.2342	-0.1235	0.7921	-0.7784	-0.0362	0.1184	0.3486	-0.0134	0.0756	0.0549	-0.0541	0.2431	16.3984	-9.9681	-16.0294
18	0.49	0.3719	0.3124	0.2675	0.2052	1.6881	-0.0268	-0.0162	0.0628	0.3192	-0.0527	0.5388	0.0494	-0.0912	0.0707	0.17	-0.0007	0.0488	0.0448	-0.0535	0.2498	15.2748	20.2033	-18.03
19	1.4379	-0.0297	0.109	1.1528	-0.6513	0.5466	-0.3265	-0.0021	0.2311	-0.5015	0.1919	0.6036	-0.3371	-0.1102	0.1	0.2893	-0.0027	-0.0488	0.07	-0.0253	0.3021	15.9572	23.7073	-22.5138
20	0.7377	-1.1367	0.1223	1.8919	-0.1075	0.7418	-0.1702	-0.0756	-0.1643	0.5498	-0.0647	0.2936	-0.0984	-0.1558	0.2002	0.2688	-0.0145	0.13	0.0439	-0.0399	0.1788	15.5637	21.3751	-12.3981
21	1.4275	-0.771	-0.1757	1.8346	0.3874	0.5601	0.164	0.0899	-0.3194	0.5121	0.1114	0.7302	0.1946	-0.1501	-0.2307	0.323	-0.0308	0.0582	0.0999	0.0517	0.2755	18.9694	15.3778	-12.8378

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 728:755)	A	728 - 755
2	X-RAY DIFFRACTION	2	(chain A and resid 756:781)	A	756 - 781
3	X-RAY DIFFRACTION	3	(chain A and resid 782:802)	A	782 - 802
4	X-RAY DIFFRACTION	4	(chain A and resid 803:808)	A	803 - 808
5	X-RAY DIFFRACTION	5	(chain B and resid 728:748)	B	728 - 748
6	X-RAY DIFFRACTION	6	(chain B and resid 749:786)	B	749 - 786
7	X-RAY DIFFRACTION	7	(chain B and resid 787:801)	B	787 - 801
8	X-RAY DIFFRACTION	8	(chain B and resid 802:807)	B	802 - 807
9	X-RAY DIFFRACTION	9	(chain C and resid 722:729)	C	722 - 729
10	X-RAY DIFFRACTION	10	(chain C and resid 730:755)	C	730 - 755
11	X-RAY DIFFRACTION	11	(chain C and resid 756:771)	C	756 - 771
12	X-RAY DIFFRACTION	12	(chain C and resid 772:801)	C	772 - 801
13	X-RAY DIFFRACTION	13	(chain C and resid 802:807)	C	802 - 807
14	X-RAY DIFFRACTION	14	(chain D and resid 727:755)	D	727 - 755
15	X-RAY DIFFRACTION	15	(chain D and resid 756:771)	D	756 - 771
16	X-RAY DIFFRACTION	16	(chain D and resid 772:801)	D	772 - 801
17	X-RAY DIFFRACTION	17	(chain D and resid 802:807)	D	802 - 807
18	X-RAY DIFFRACTION	18	(chain E and resid 729:758)	E	729 - 758
19	X-RAY DIFFRACTION	19	(chain E and resid 759:771)	E	759 - 771
20	X-RAY DIFFRACTION	20	(chain E and resid 772:800)	E	772 - 800
21	X-RAY DIFFRACTION	21	(chain E and resid 801:808)	E	801 - 808

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