PDB-2q2i: Crystal structure of the protein secretion chaperone CsaA from Ag...

ID or keywords:

Entry

Database: PDB / ID: 2q2i

Title

Crystal structure of the protein secretion chaperone CsaA from Agrobacterium tumefaciens.

Components

Secretion chaperone

Keywords

CHAPERONE / beta barrel / OB fold / homodimer / protein secretion

Function / homology

Function and homology information

methionyl glutamyl tRNA synthetase complex / tyrosine-tRNA ligase activity / tRNA binding
Similarity search - Function

Biological species

Agrobacterium tumefaciens str. C58 (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Feldman, A.R. / Shapova, Y.A. / Paetzel, M.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Phage display and crystallographic analysis reveals potential substrate/binding site interactions in the protein secretion chaperone CsaA from Agrobacterium tumefaciens.
Authors: Feldman, A.R. / Shapova, Y.A. / Wu, S.S. / Oliver, D.C. / Heller, M. / McIntosh, L.P. / Scott, J.K. / Paetzel, M.

History

Deposition	May 28, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 1, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.2	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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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PDBx/mmCIF format	2q2i.cif.gz	67.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2q2i_validation.pdf.gz	447.6 KB	Display	wwPDB validaton report
Full document	2q2i_full_validation.pdf.gz	447.5 KB	Display
Data in XML	2q2i_validation.xml.gz	14.3 KB	Display
Data in CIF	2q2i_validation.cif.gz	21.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q2/2q2i ftp://data.pdbj.org/pub/pdb/validation_reports/q2/2q2i	HTTPS FTP

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Related structure data

Related structure data	2q2hC 1gd7S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3qub-d 3qu7-1 1mkh-1 3qxg-3 6hyy-1 2fdr-d 3qxg-4 1j97-1 6q6j-1 3qx7-d 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
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (3)

Deposited unit

A: Secretion chaperone

B: Secretion chaperone

hetero molecules

25.4 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)	60.653, 60.653, 113.389
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Secretion chaperone / AGR_C_4014p Mass: 12518.390 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria) Species: Agrobacterium tumefaciens / Strain: C58/ATCC 33970 / Gene: csaA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UDB9, UniProt: A9CI62*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.4 Å³/Da / Density % sol: 48.81 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.8M ammonium sulfate, 0.1M HEPES pH 7.5, 2% PEG400, 5% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 24, 2004 / Details: VariMax Cu HF
Radiation	Monochromator: nickel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.55→52.53 Å / Num. all: 34123 / Num. obs: 34123 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.82 % / R_merge(I) obs: 0.04 / Χ²: 0.91 / Net I/σ(I): 23.7 / Scaling rejects: 3310
Reflection shell	Resolution: 1.55→1.61 Å / Redundancy: 10.13 % / R_merge(I) obs: 0.341 / Mean I/σ(I) obs: 7.2 / Num. measured all: 35222 / Num. unique all: 3400 / Χ²: 4.6 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
d*TREK	8.0SSI	data scaling
REFMAC	5.2.0005	refinement
PDB_EXTRACT	2	data extraction
CrystalClear		data collection
CrystalClear		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1GD7

1gd7

Resolution: 1.55→52.53 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.943 / SU B: 2.894 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.208	1727	5.1 %	RANDOM
R_work	0.178	-	-	-
obs	0.18	34099	99.7 %	-
all	-	34099	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 7.929 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	-0.11 Å²	0 Å²
2-	-	-0.21 Å²	0 Å²
3-	-	-	0.32 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→52.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1677	0	25	350	2052

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	1731
X-RAY DIFFRACTION	r_angle_refined_deg	1.282	1.993	2341
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.318	5	218
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.975	24.118	68
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.815	15	281
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.079	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	267
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1295
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	745
X-RAY DIFFRACTION	r_nbtor_refined	0.312	0.2	1206
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.111	0.2	258
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.186	0.2	36
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.118	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	0.546	1.5	1128
X-RAY DIFFRACTION	r_mcangle_it	0.828	2	1800
X-RAY DIFFRACTION	r_scbond_it	1.473	3	654
X-RAY DIFFRACTION	r_scangle_it	2.218	4.5	541

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.613	126	-
R_work	0.508	2389	-
obs	-	2515	99.56 %

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	7.4738	6.3385	-6.3263	17.1546	-9	10.8174	-0.0728	0.1546	-0.0877	-0.6764	0.0143	0.0016	0.4213	-0.1535	0.0585	0.0638	0.0077	-0.0053	0.0545	-0.0159	-0.0396	-37.708	-7.385	10.37
2	11.7907	1.9314	-3.928	2.5792	1.3726	7.5105	0.1033	-0.1248	0.5182	-0.013	0.041	0.0055	-0.16	0.3571	-0.1443	0.0484	0.022	0.0157	0.0222	-0.0017	-0.0257	-31.576	-2.715	8.368
3	0.2373	-0.566	1.0129	1.3883	-1.606	21.5876	-0.1822	-0.1375	0.0378	0.0037	-0.102	0.061	-0.3451	-0.3546	0.2842	0.0333	0.0028	0.002	0.0711	-0.0149	-0.0145	-26.191	-2.754	-0.796
4	6.3061	-4.7119	-2.6839	9.2579	3.8875	2.8306	-0.0461	-0.1089	0.0594	0.1069	0.1141	-0.3389	0.025	0.1144	-0.068	0.0516	0.0076	0.0113	0.0265	0.0107	-0.0289	-17.079	-7.1	-13.573
5	4.7545	-3.1924	1.5686	9.6178	-4.102	12.109	0.0127	-0.1942	0.0932	-0.0881	-0.2496	-0.4062	0.4365	0.677	0.2369	0.0261	0.0138	0.0016	0.0283	0.0059	-0.0327	-10.887	-20.696	-9.869
6	13.0995	-6.5173	6.8659	13.6765	-5.5115	9.4785	0.3297	-0.6468	-0.7067	0.5669	0.2395	0.9572	0.2858	-0.0274	-0.5692	0.0936	-0.0001	-0.0042	0.033	0.0199	0.0074	-16.555	-24.659	-7.347
7	0.7535	-3.3599	-0.5935	20.3817	0.793	4.0701	0.0224	-0.0515	0.0823	0.1946	-0.0367	-0.6556	0.0808	0.1001	0.0143	0.0391	0.0029	-0.0011	0.0264	0.0082	-0.0055	-15.265	-8.256	-9.73
8	10.8351	9.7717	8.364	23.6062	2.337	8.4951	-0.3725	-0.4432	0.6839	0.1922	-0.1814	0.5437	-0.516	0.1338	0.5539	0.0555	0.0033	-0.0026	0.0186	-0.0214	-0.0043	-18.599	2.443	-5.239
9	2.1594	2.5876	0.7189	16.9512	1.6597	0.8498	0.1698	-0.0799	0.0103	0.0993	-0.4136	-0.3947	0.0441	-0.0104	0.2438	0.0495	0.0084	0.0037	0.0282	0.0123	-0.0197	-15.215	-9.048	-5.704
10	1.9543	1.5569	-2.1266	4.982	-0.2064	2.9165	0.0592	0.1182	-0.1436	0.1019	-0.0206	-0.1019	0.0258	-0.0412	-0.0386	0.028	0.0011	0.0156	0.0153	-0.0069	-0.0263	-23.088	-20.125	-13.68
11	2.3232	-3.7226	-2.4485	14.7366	3.263	2.6303	0.3173	0.2711	-0.1301	-0.3794	-0.3645	0.1583	-0.1796	0.0697	0.0473	0.0453	0.0194	-0.016	0.0649	0.0082	-0.0336	-18.798	-12.497	-18.696
12	0.6142	0.4962	0.0031	1.8094	-1.8038	6.3231	-0.0877	-0.0118	0.1191	-0.1163	0.0942	-0.0125	0.1761	-0.2067	-0.0065	0.0403	-0.0015	0.0055	0.0289	0.0015	-0.0232	-25.357	-7.315	-9.087
13	4.5677	-2.9446	-0.6357	2.9834	1.0262	2.4641	-0.1036	-0.3131	-0.0539	0.1853	0.1097	-0.0375	0.1793	0.0037	-0.0061	0.0238	-0.0003	-0.0032	0.0682	-0.0138	-0.0416	-18.095	-9.092	4.06
14	4.4469	-0.6078	-0.2147	2.3232	-2.6172	3.1371	0.0139	0.0505	-0.0077	-0.1607	-0.0361	0.0378	0.0434	0.0225	0.0222	0.0409	0.0109	-0.0166	0.0333	0.0054	-0.0301	-10.32	-15.447	-0.371
15	14.6022	1.8898	1.8034	0.2863	0.4727	1.5941	-0.1193	-0.1421	0.1334	-0.0283	0.0124	0.0627	-0.0638	0.0303	0.1069	0.0365	0.0014	0.0017	0.0196	0.0021	-0.0227	-21.594	-10.847	-2.762
16	4.9274	-2.5422	-0.2495	8.3028	3.5985	5.0881	-0.1322	0.1575	-0.4934	0.1304	-0.0537	0.2016	0.2858	-0.0235	0.1859	0.028	-0.027	0.041	0.0121	-0.0103	0.0163	-32.504	-22.735	-8.428
17	1.6605	-1.6546	0.2984	16.1093	0.7134	0.5555	0.0463	0.0552	-0.1901	0.1717	-0.0654	0.0737	0.0031	-0.0765	0.0191	0.0263	-0.0065	0.0144	0.0333	-0.0132	-0.0168	-28.753	-16.816	-10.051
18	8.3408	4.9629	3.4936	4.2392	2.0429	4.3088	-0.0746	-0.0557	0.2263	-0.0874	0.1298	-0.0056	-0.0241	-0.2186	-0.0552	0.0147	0.0153	-0.0031	0.0464	0.0075	-0.0291	-32.018	-0.781	-14.188
19	13.1153	1.2904	-7.3087	1.4549	-0.6207	4.081	0.1437	-0.1522	0.2983	-0.002	-0.0282	0.1942	-0.1849	-0.0513	-0.1156	0.0119	0.0006	0.0035	0.0319	-0.0039	-0.0333	-28.752	0.74	-4.224
20	11.9852	7.4513	-2.1223	37.2751	-7.1862	7.0632	-0.4339	-0.2077	-0.1965	-0.7395	0.5323	-0.2682	0.0833	0.1861	-0.0984	0.0057	0.0558	-0.004	0.1439	-0.0664	-0.1093	-22.131	-7.33	8.358
21	21.2075	7.0294	3.8772	3.2269	4.9387	15.5923	-0.296	-0.1662	-0.505	0.1235	0.3159	0.0778	0.3261	0.4149	-0.0199	0.0714	0.0633	0.0059	0.0257	0.0193	-0.0469	-28.422	-12.032	9.017
22	1.9667	1.0911	3.3042	4.0679	4.4836	7.6423	0.1039	0.0303	-0.0016	0.0973	-0.0562	0.0039	0.2351	0.1289	-0.0477	0.0515	-0.0068	0.0034	0.0647	-0.0049	-0.0269	-36.549	-13.376	1.313
23	5.5174	-2.6871	1.7237	1.7751	-1.2786	2.3686	0.1665	0.0007	0.1189	-0.0515	-0.2122	-0.0047	-0.0321	-0.0124	0.0457	0.0138	-0.0063	-0.0218	0.015	-0.0101	-0.0125	-48.879	-10.381	-8.996
24	15.7504	-7.6399	-2.2647	4.0273	0.1412	3.1762	-0.0703	-0.7899	1.8472	-0.0769	-0.0411	0.5382	-0.2232	-0.2281	0.1114	0.0073	0.0302	-0.0548	-0.0158	-0.0888	0.2204	-52.713	4.016	-6.212
25	3.263	-2.021	1.0182	10.159	-1.1061	0.8932	-0.0343	-0.1128	0.207	-0.0132	-0.0059	0.221	-0.0508	-0.0736	0.0402	0.0248	-0.0068	0.0102	0.0279	-0.0304	-0.0141	-48.448	-7.65	-4.99
26	7.1116	0.0946	1.4167	11.7636	-1.0571	9.5386	-0.0186	-0.4686	-0.1599	0.1505	0.0825	-0.2772	0.2971	0.0465	-0.0639	0.0266	-0.0168	0.0152	0.0453	-0.0094	-0.0102	-46.556	-19.301	0.141
27	2.2878	4.5971	-4.0079	16.6233	-6.5725	7.318	0.3401	-0.1952	0.2837	0.6372	-0.3425	0.2418	-0.3135	0.1874	0.0023	0.0077	-0.0106	0.0012	0.0525	-0.0261	0.035	-47.166	-3.578	-1.781
28	9.6407	2.8896	-1.7469	3.3408	-1.7372	0.9117	0.1289	0.4029	0.7131	0.035	0.1703	0.3203	0.0907	0.0985	-0.2992	-0.0136	0.0314	-0.0041	0.0445	0.0751	0.034	-43.251	2.056	-13.399
29	2.4734	5.206	-0.0352	24.6383	-4.0768	1.1716	0.1388	0.5332	0.2891	-0.5304	0.0054	0.7846	0.213	-0.0194	-0.1442	0.0117	0.0245	-0.0331	0.0886	0.0282	-0.0286	-48.28	-5.578	-15.072
30	1.5065	0.8203	-1.0442	2.7871	2.9352	5.9689	-0.1078	0.0172	0.0337	-0.1549	0.0226	0.0125	-0.1084	0.0651	0.0851	0.0329	0.0145	-0.0027	0.0185	0.0061	-0.0236	-39.738	-9.849	-7.027
31	7.6351	-5.8191	-1.729	4.806	1.6857	0.7902	-0.2263	0.0067	0.1397	0.4207	-0.0008	0.2081	0.0924	0.0546	0.227	0.0395	-0.0054	0.0156	0.0211	-0.0237	-0.0088	-44.853	-5.972	8.087
32	10.2874	-9.476	0.0026	28.1053	6.8315	6.8433	-0.0342	-0.1214	-0.1025	0.1815	-0.5291	0.4799	0.1084	-0.3277	0.5633	0.0027	-0.0325	0.0278	0.0534	-0.0533	0.0165	-53.232	-1.936	3.94
33	10.9954	2.2436	-3.8013	1.3957	0.444	2.9003	0.0753	-0.1578	0.0014	0.06	-0.1352	0.0146	0.0452	0.0668	0.0599	0.0272	-0.0141	-0.0013	0.0212	-0.004	-0.0113	-41.743	-5.493	-0.369
34	14.7709	-11.0226	4.2636	13.7496	-6.9524	10.6648	0.1318	0.3993	1.3138	-0.0259	-0.3003	-0.3243	-0.1779	0.2215	0.1684	-0.009	-0.0054	0.0165	0.0028	0.0621	0.0626	-32.907	5.467	-9.879
35	2.3269	-0.1789	0.0381	9.5763	-1.526	0.5742	0.111	0.0828	0.2831	0.0657	-0.1274	0.4179	0.0045	0.0587	0.0164	0.0295	0.0103	0.0173	0.0385	0.0209	0.0003	-36.876	-0.557	-9.828
36	7.8346	1.4726	-3.059	6.233	-2.5472	1.8474	-0.0091	-0.0813	-0.0648	-0.0533	-0.024	0.1534	0.0111	0.0765	0.0331	0.0336	-0.0095	0.007	0.0708	-0.0163	-0.0478	-34.601	-17.056	-12.832
37	21.5418	2.5819	2.3955	1.8379	0.4698	1.6598	0.067	-0.1047	0.1509	-0.0093	-0.0964	-0.0716	0.1359	0.1569	0.0294	0.0313	-0.011	0.0165	0.0338	-0.0049	-0.0375	-35.189	-17.617	-2.273

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 7	5 - 10
2	X-RAY DIFFRACTION	2	A	A	8 - 12	11 - 15
3	X-RAY DIFFRACTION	3	A	A	13 - 17	16 - 20
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