PDB-4nrh: CopN-Scc3 complex

ID or keywords:

Entry

Database: PDB / ID: 4nrh

Title

CopN-Scc3 complex

Components

Chaperone SycD
CopN

Keywords

Chaperone/protein binding / cytosol / Chaperone-protein binding complex

Function / homology

Function and homology information

protein secretion by the type III secretion system / outer membrane / negative regulation of protein secretion / cell surface
Similarity search - Function

Biological species

Chlamydia pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Archuleta, T.L. / Spiller, B.W.

Citation

Journal: Plos Pathog. / Year: 2014
Title: A gatekeeper chaperone complex directs translocator secretion during type three secretion.
Authors: Archuleta, T.L. / Spiller, B.W.

History

Deposition	Nov 26, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 15, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 4, 2015	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4nrh.cif.gz	383.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4nrh.ent.gz	316.2 KB	Display	PDB format
PDBx/mmJSON format	4nrh.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/nr/4nrh ftp://data.pdbj.org/pub/pdb/validation_reports/nr/4nrh	HTTPS FTP

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Related structure data

Similar structure data	1klf-3 2wvr-d 1klf-2 5n47-3 2771 1klf-4 6sit-d 3e20-4 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CopN

B: Chaperone SycD

C: CopN

D: Chaperone SycD

hetero molecules

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

1

A: CopN

D: Chaperone SycD

hetero molecules

defined by author&software
56.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Chaperone SycD

C: CopN

hetero molecules

defined by author&software
56.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.571, 96.183, 94.472
Angle α, β, γ (deg.)	90.00, 92.27, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

#1: Protein	CopN / Low Calcium Response E / Low calcium response E / Type III secreted protein SctW Mass: 35420.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia pneumoniae (bacteria) / Gene: copN, CpB0334, CPn_0324, CP_0433, lcrE / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL32 (DE3) / References: UniProt: Q9Z8L4
#2: Protein	Chaperone SycD / Low Calcium Response Protein H / Low calcium response protein H / Type III secretion chaperone Mass: 20984.713 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia pneumoniae (bacteria) / Gene: CpB1060, CPn_1021, CP_0832, lcrH_2, Scc3 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9Z6N8
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.48 Å³/Da / Density % sol: 50.36 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 200mM Na/K Tartate, 18-22 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 55841 / Num. obs: 50257 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / B_iso Wilson estimate: 32 Å² / R_merge(I) obs: 0.059 / R_sym value: 0.081 / Net I/σ(I): 24.2
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.553 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1480 / R_sym value: 0.722 / % possible all: 53.7

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Processing

Software

Name	Version	Classification
MD2		data collection
PHENIX	(phenix.refine: 1.8.4_1496)	model building
PHENIX		refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.8.4_1496	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.2→47.199 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 26.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2267	1982	3.94 %
R_work	0.1836	-	-
obs	0.1853	46421	88.91 %

Solvent computation

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

Refine analyze

Luzzati sigma a obs: 0.26 Å

Refinement step

Cycle: LAST / Resolution: 2.2→47.199 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7302	0	2	377	7681

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7452
X-RAY DIFFRACTION	f_angle_d	0.567	10094
X-RAY DIFFRACTION	f_dihedral_angle_d	12.81	2762
X-RAY DIFFRACTION	f_chiral_restr	0.023	1125
X-RAY DIFFRACTION	f_plane_restr	0.003	1303

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 (%)
2.1906-2.2454	0.35	75	0.2635	1807	X-RAY DIFFRACTION	47
2.2454-2.3061	0.2923	98	0.2416	2300	X-RAY DIFFRACTION	59
2.3061-2.374	0.2869	116	0.2345	2611	X-RAY DIFFRACTION	68
2.374-2.4506	0.2442	113	0.2299	3025	X-RAY DIFFRACTION	78
2.4506-2.5382	0.2852	158	0.2198	3566	X-RAY DIFFRACTION	92
2.5382-2.6398	0.2901	154	0.2281	3856	X-RAY DIFFRACTION	100
2.6398-2.7599	0.3132	158	0.2207	3876	X-RAY DIFFRACTION	100
2.7599-2.9054	0.2998	163	0.2184	3872	X-RAY DIFFRACTION	100
2.9054-3.0874	0.2507	152	0.2077	3902	X-RAY DIFFRACTION	100
3.0874-3.3257	0.218	161	0.1956	3867	X-RAY DIFFRACTION	100
3.3257-3.6603	0.1999	157	0.1765	3907	X-RAY DIFFRACTION	100
3.6603-4.1897	0.1972	155	0.1562	3893	X-RAY DIFFRACTION	100
4.1897-5.2774	0.1777	169	0.1501	3900	X-RAY DIFFRACTION	100
5.2774-47.2097	0.2116	153	0.1608	3975	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	2.9176	-1.1911	0.7096	5.2981	-3.3067	4.6898	-0.1198	-0.2777	-0.2275	0.1401	0.2998	0.1821	0.2348	-0.1312	-0.1585	0.2549	0.0068	-0.0077	0.2205	-0.017	0.2853	14.6548	33.9362	42.7664
2	4.9425	-2.6879	1.1152	5.1731	-1.7904	3.476	-0.2227	-0.4767	-0.0402	0.4368	0.288	-0.0947	-0.3	-0.4001	-0.0852	0.2793	0.0512	-0.0132	0.299	-0.0148	0.219	1.0896	54.8098	33.6544
3	6.1499	1.7604	0.0182	4.0918	-0.7882	7.1901	-0.3705	0.1901	-0.6643	-0.4772	0.3616	-0.69	0.5618	-0.1039	0.0363	0.3455	0.0548	-0.0549	0.2634	0.0033	0.2987	2.4821	47.3639	27.1662
4	2.4063	3.0481	-1.0238	3.3108	-1.0249	1.4654	-0.1065	0.1314	-0.1728	-0.1235	0.0424	-0.4432	-0.0206	0.1119	0.0001	0.3215	-0.0107	-0.1096	0.3137	0.0021	0.291	0.1696	65.6284	21.2266
5	3.3976	-0.4601	0.6828	7.7414	-2.6529	5.234	0.3422	-0.5886	-0.0607	0.8638	-0.0753	0.5416	0.084	-0.558	-0.2533	0.5491	0.0287	-0.0787	0.3878	0.0108	0.3748	-7.1191	75.5767	22.2969
6	5.5155	5.6644	5.1034	5.8371	5.2405	4.7104	0.2521	-0.9521	1.0014	0.0422	-0.1253	0.7859	-0.7716	-0.933	-0.0533	0.5289	0.1666	-0.0022	0.4708	-0.032	0.4385	-11.6071	82.7651	19.8494
7	1.1698	0.353	0.6848	5.7271	2.1869	1.5857	-0.0584	0.0167	0.0791	0.1372	0.0693	-0.3593	-0.1285	0.0054	-0.0237	0.3583	-0.0227	-0.0566	0.2852	0.0572	0.2711	-4.3256	72.8443	13.099
8	6.7253	-0.0912	0.2106	3.3123	4.8807	7.3777	-0.3874	-0.3206	0.676	-1.1508	-0.1121	1.2046	-0.4418	-0.3036	0.3995	0.5526	-0.0101	-0.1752	0.4628	0.0177	0.3999	-12.0926	77.4112	8.1502
9	4.8051	-1.0948	1.158	3.1833	-0.6105	5.8663	-0.2577	-0.6202	0.1781	0.337	0.2281	0.1082	-0.2606	-0.0539	0.0495	0.2599	-0.0385	-0.0046	0.2393	-0.0253	0.3171	36.2342	58.0838	50.5169
10	3.5776	-2.5177	-0.5524	6.1308	3.3883	2.3613	-0.113	0.1708	-0.042	0.329	0.415	-0.0907	0.7086	-0.2655	-0.2424	0.2549	-0.0111	-0.0409	0.2653	0.0233	0.2934	32.4122	45.6619	42.5229
11	4.2135	-0.2526	0.003	4.9991	-1.4809	3.8412	-0.0126	-0.1005	0.5002	-0.1893	0.087	0.3955	-0.3308	-0.0959	-0.0612	0.2722	-0.0231	-0.0512	0.247	-0.0265	0.3705	27.3667	62.4598	40.1505
12	1.6841	0.3688	-0.7598	3.987	-0.8961	2.8755	-0.1052	0.2784	0.0251	-0.2978	-0.0413	-0.3945	-0.3576	0.3052	0.1696	0.2938	-0.0912	-0.026	0.3083	0.0667	0.2802	31.4951	56.928	30.1939
13	2.6191	0.87	0.1637	6.5089	-0.6211	4.0212	-0.4823	1.3967	-0.1011	-1.3956	0.6302	-0.4071	0.0589	0.4863	-0.0446	0.5549	-0.1926	0.0162	0.7752	-0.0472	0.3805	29.2134	54.0773	17.195
14	6.3439	-1.571	-1.1999	5.9157	0.7046	7.7588	0.0564	1.3654	0.5409	-1.6434	0.2381	1.0994	-0.3001	-0.6967	-0.1758	0.7575	-0.206	-0.2038	0.7995	0.063	0.5454	18.0065	55.0598	12.7047
15	2.4502	1.1821	1.952	3.1014	3.1017	3.7296	-0.2	0.0563	0.1964	0.1136	0.1736	-0.0129	-0.2924	0.2838	0.0245	0.5278	-0.0044	-0.0416	0.2822	0.023	0.2735	58.4961	69.6193	73.3621
16	1.1404	0.5534	0.2366	5.8297	-0.7258	1.4791	0.0362	0.0721	-0.166	0.1666	-0.0106	-0.272	-0.0096	0.1464	-0.0594	0.2009	0.0154	-0.0173	0.2746	-0.0367	0.2566	47.2055	37.7374	50.4011
17	4.8037	-0.0058	0.9978	8.2437	1.9933	2.0637	0.4161	0.2149	-0.6947	-0.8258	0.4659	-0.8552	0.6363	0.8904	-0.7712	0.6732	0.0757	-0.0414	0.5553	0.023	0.4396	4.8031	49.6219	4.1112
18	4.669	-1.0792	1.6273	2.5458	-0.8238	5.0511	-0.1883	-0.1589	0.1474	0.0796	0.1441	-0.0716	-0.0748	-0.2807	0.0612	0.4181	-0.0629	0.0022	0.3045	-0.0181	0.2199	-5.559	60.4398	5.6309
19	6.9872	3.8309	-0.131	7.8717	0.6394	4.6029	-0.1344	0.5037	-0.4179	-0.2399	0.0463	0.0893	0.4984	0.373	0.1858	0.7445	0.0163	-0.0353	0.4181	0.0046	0.2678	-2.6616	48.5482	-8.111
20	4.1433	-0.5082	1.0532	2.5994	0.8315	4.1067	0.1386	-0.0051	-0.2076	-0.0744	-0.0735	0.2958	0.3623	-0.6212	-0.0704	0.5302	-0.1634	-0.0311	0.4371	0.0422	0.2408	-14.1924	52.4014	-4.8905
21	5.845	-0.6644	5.3483	2.7294	-0.0021	7.5925	0.0286	-1.7263	-0.5087	0.7214	0.1682	0.7437	0.6136	-1.9735	-0.2484	0.7445	-0.2066	-0.0701	1.2127	0.0985	0.5373	-28.7582	52.1556	-9.9152
22	8.8889	2.6903	0.1877	6.7915	1.1515	5.8123	-0.6004	0.7659	0.556	-1.3141	0.1468	0.9383	-0.0072	-1.264	0.4183	0.708	-0.0477	-0.1355	1.0467	0.0874	0.4657	-27.5019	57.1823	-21.3166

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 94 through 195 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 196 through 229 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 230 through 256 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 257 through 294 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 295 through 321 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 322 through 336 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 337 through 361 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 362 through 382 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 29 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 30 through 50 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 51 through 83 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 84 through 117 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 118 through 152 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 153 through 170 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 94 through 256 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 257 through 380 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 13 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 14 through 50 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 51 through 66 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 67 through 122 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 123 through 139 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 140 through 170 )

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