PDB-5d6h: Crystal structure of CsuC-CsuA/B chaperone-major subunit pre-asse...

ID or keywords:

Entry

Database: PDB / ID: 5d6h

Title

Crystal structure of CsuC-CsuA/B chaperone-major subunit pre-assembly complex from Csu biofilm-mediating pili of Acinetobacter baumannii

Components

CsuA/B
CsuCCalifornia State University, Chico

Keywords

CHAPERONE/PROTEIN TRANSPORT / archaic chaperone-usher pathway /

Ig-like fold / beta sheet sandwich / donor-strand complementation / chaperone-protein transport complex

Function / homology

Function and homology information

cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.4 Å

Authors

Pakharukova, N.A. / Tuitilla, M. / Paavilainen, S. / Zavialov, A.

Funding support

Finland, 2items

Citation

Journal: Plos Pathog. / Year: 2015
Title: Structural Insight into Archaic and Alternative Chaperone-Usher Pathways Reveals a Novel Mechanism of Pilus Biogenesis.
Authors: Pakharukova, N. / Garnett, J.A. / Tuittila, M. / Paavilainen, S. / Diallo, M. / Xu, Y. / Matthews, S.J. / Zavialov, A.V.

History

Deposition	Aug 12, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 4, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 2, 2015	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5d6h.cif.gz	140.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5d6h.ent.gz	116.5 KB	Display	PDB format
PDBx/mmJSON format	5d6h.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/d6/5d6h ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d6h	HTTPS FTP

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Related structure data

Related structure data	5dfkC C: citing same article (ref.)
Similar structure data	2orp-d 4krm-6 1nos-d 6iwd-d 7ck2-2 5tuc-2 4gfl-d 2f57-2 2f57-1 1sj7-5 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CsuC

B: CsuA/B

43.1 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)	94.705, 94.705, 187.048
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	181
Space group name H-M	P6₄22

Components on special symmetry positions

ID	Model	Components
1	1	A-351- HOH
2	1	A-384- HOH
3	1	A-395- HOH

#1: Protein	CsuC / California State University, Chico Mass: 27192.264 Da / Num. of mol.: 1 / Fragment: UNP residues 35-277 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: csuC / Plasmid: pET101 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q6XBY4
#2: Protein	CsuA/B Mass: 15930.395 Da / Num. of mol.: 1 / Fragment: UNP residues 38-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: csuA/B / Plasmid: pET101 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q6XBY7
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.49 Å³/Da / Density % sol: 64.75 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M sodium malonate, 15% PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 23, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9792	1
2	0.979	1

Reflection

Resolution: 2.4→46.762 Å / Num. all: 20138 / Num. obs: 36640 / % possible obs: 99.8 % / Redundancy: 15.2 % / R_pim(I) all: 0.014 / R_rim(I) all: 0.054 / R_sym value: 0.043 / Net I/av σ(I): 8.978 / Net I/σ(I): 37.4 / Num. measured all: 305639

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_sym value	Net I/σ(I) obs	% possible all
2.4-2.53	16.3	0.539	1.4	46837	2869	0.135	0.539	6.3	100
2.53-2.68	16	0.308	2.4	43399	2718	0.078	0.308	10.5	100
2.68-2.87	14.9	0.194	3.8	38393	2578	0.052	0.194	14.6	100
2.87-3.1	15.9	0.099	7.5	38031	2389	0.026	0.099	25.7	100
3.1-3.39	15.7	0.055	13	34836	2222	0.015	0.055	41.9	99.8
3.39-3.79	14.3	0.039	17.4	29142	2036	0.012	0.039	55.7	100
3.79-4.38	15.2	0.032	19.1	27407	1801	0.01	0.032	70	99.8
4.38-5.37	14.1	0.029	21.3	21793	1551	0.01	0.029	79.6	99.6
5.37-7.59	13.8	0.029	21.1	16877	1226	0.012	0.029	74.1	99.1
7.59-46.762	11.9	0.029	14.6	8924	748	0.013	0.029	81	97.8

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Processing

Software

Name	Version	Classification
PHENIX		refinement
SCALA	3.3.20	data scaling
PDB_EXTRACT	3.15	data extraction
PHENIX		phasing
XDS		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 2.4→45.904 Å / FOM work R set: 0.8107 / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.83 / Phase error: 25.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2658	3647	9.97 %
R_work	0.219	32941	-
obs	0.2237	36588	99.64 %

Solvent computation

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

Displacement parameters

B_iso max: 133.01 Å² / B_iso mean: 46.82 Å² / B_iso min: 8.41 Å²

Refinement step

Cycle: final / Resolution: 2.4→45.904 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2455	0	0	158	2613
B_iso mean	-	-	-	41.63	-
Num. residues	-	-	-	-	321

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2492
X-RAY DIFFRACTION	f_angle_d	1.245	3364
X-RAY DIFFRACTION	f_chiral_restr	0.076	395
X-RAY DIFFRACTION	f_plane_restr	0.005	422
X-RAY DIFFRACTION	f_dihedral_angle_d	14.918	892

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4001-2.4317	0.294	135	0.2398	1303	1438	100
2.4317-2.465	0.3258	140	0.2563	1252	1392	100
2.465-2.5002	0.3872	145	0.2688	1278	1423	100
2.5002-2.5375	0.3631	136	0.2467	1252	1388	100
2.5375-2.5772	0.3306	142	0.2594	1258	1400	100
2.5772-2.6194	0.3211	145	0.2444	1294	1439	100
2.6194-2.6646	0.2618	139	0.2359	1266	1405	100
2.6646-2.713	0.3194	141	0.2377	1282	1423	100
2.713-2.7652	0.2609	137	0.2213	1267	1404	100
2.7652-2.8216	0.3163	137	0.2546	1255	1392	100
2.8216-2.883	0.3415	143	0.2413	1290	1433	100
2.883-2.95	0.2595	141	0.2397	1264	1405	100
2.95-3.0238	0.2718	142	0.2296	1262	1404	100
3.0238-3.1055	0.2589	138	0.2201	1271	1409	100
3.1055-3.1969	0.232	143	0.2095	1263	1406	100
3.1969-3.3001	0.2268	142	0.2109	1270	1412	100
3.3001-3.418	0.2725	138	0.2101	1284	1422	100
3.418-3.5548	0.2864	135	0.206	1265	1400	100
3.5548-3.7165	0.2556	144	0.2042	1262	1406	100
3.7165-3.9123	0.2448	137	0.2041	1277	1414	100
3.9123-4.1573	0.2375	143	0.2008	1258	1401	100
4.1573-4.478	0.2091	139	0.179	1276	1415	100
4.478-4.9282	0.1893	141	0.1615	1256	1397	99
4.9282-5.6402	0.2503	142	0.2083	1248	1390	99
5.6402-7.1018	0.2723	142	0.2431	1242	1384	98
7.1018-45.9127	0.2832	140	0.2544	1246	1386	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	1.2243	-0.6795	0.4083	1.9684	-0.0163	0.8835	-0.1387	-0.1886	0.0669	0.1823	0.1346	0.0497	-0.1076	-0.0782	0.0642	0.4243	0.2617	0.0368	0.1283	-0.034	0.1805	38.834	13.1842	103.162
2	7.5294	-3.3124	-2.4339	8.4948	2.6475	2.7961	-0.22	-0.2621	-0.6564	0.7608	-0.1034	0.8939	0.1557	-0.2351	0.3648	0.4862	0.0009	0.0548	0.1338	0.0104	0.2526	31.5743	4.8665	100.0848
3	3.1319	2.0552	0.3288	7.9822	3.3429	2.5907	-0.0757	-0.186	-0.0909	0.1627	0.2666	-0.4951	-0.0989	0.1278	-0.185	0.3634	0.1926	0.0347	0.183	-0.0327	0.1764	50.4979	8.7458	104.8519
4	4.966	-0.3713	3.3913	4.0086	0.6031	5.6843	0.2473	0.5094	-0.4208	-0.8436	-0.1055	0.3736	-0.0067	-0.3025	-0.1326	0.4291	0.0449	-0.0452	0.1885	-0.0339	0.2025	32.3534	8.3959	89.3524
5	0.3214	-0.2199	-0.8634	0.8332	1.1747	2.8086	-0.353	-0.5063	0.1707	0.4878	0.2499	-0.1816	0.1934	0.1791	0.1026	0.5475	0.3293	-0.0152	0.3749	-0.0848	0.2163	37.7655	10.2671	112.5766
6	2.5771	-1.8904	1.0534	3.5668	-1.3222	2.7867	-0.0446	0.1362	0.2156	-0.1603	-0.1233	-0.0692	-0.0729	-0.038	0.1929	0.3187	0.2661	-0.026	0.1225	0.0379	0.2167	32.5445	17.5798	94.7392
7	5.5576	-1.8203	-0.8174	3.4212	-1.5346	5.6256	-0.0072	0.1115	0.1712	-0.0442	-0.0356	0.0115	-0.1854	-0.303	0.0046	0.4732	0.2806	-0.132	0.5156	0.0896	0.4531	21.6089	25.3193	91.6801
8	2.8462	-1.7754	-0.0244	3.5885	0.4243	0.0698	-0.2427	-0.4736	-0.0429	0.5909	0.2917	0.2829	-0.0545	-0.2211	-0.0814	0.5292	0.5011	0.0217	0.5004	0.065	0.4134	18.8606	26.5484	105.1411
9	4.7996	-4.2523	-3.8959	4.746	4.2793	3.9689	-0.2357	-0.5062	0.0962	0.4393	0.3355	0.0276	-0.0316	0.0704	-0.0813	0.6436	0.4581	0.1678	0.8526	0.049	0.6151	12.6709	27.1073	112.4134
10	5.7312	-3.7253	-0.8477	2.8125	0.933	0.5025	0.0549	0.1306	0.0695	0.0594	-0.0356	0.2328	-0.25	-0.3557	-0.0395	0.7062	0.4843	0.0186	0.5544	0.0964	0.596	19.2128	31.8955	100.2451
11	1.142	0.1236	-0.3826	2.3055	-2.9147	4.1619	0.0925	-0.7188	0.2857	0.2279	0.3305	0.1306	-0.4704	0.1471	-0.4367	0.6763	0.3046	0.008	0.7105	-0.225	0.6269	41.1481	21.8811	119.574
12	1.3967	-0.8472	-0.658	1.264	0.6555	0.8415	0.0103	-0.4276	0.1119	0.238	0.1647	-0.0315	0.1029	0.113	-0.0928	0.5689	0.7304	0.0938	0.6373	-0.2498	0.3453	33.6763	18.6418	123.647

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 47 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 48 through 58 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 59 through 72 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 73 through 84 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 85 through 115 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 116 through 132 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 133 through 154 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 155 through 200 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 201 through 216 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 217 through 239 )	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 7 through 66 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 67 through 152 )	B

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