PDB-2q2h: Crystal structure of the protein secretion chaperone CsaA from Ag...

ID or keywords:

Entry

Database: PDB / ID: 2q2h

Title

Crystal structure of the protein secretion chaperone CsaA from Agrobacterium tumefaciens with a genetically fused phage-display derived peptide substrate at the N-terminus.

Components

Secretion chaperone, phage-display derived peptide

Keywords

CHAPERONE /

beta barrel / OB fold /

homodimer /

protein secretion

Function / homology

Function and homology information

tRNA binding
Similarity search - Function

Biological species

Agrobacterium tumefaciens str. C58 (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.65 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 ...Advisory / Derived calculations / Refinement description / 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 999

SEQUENCE The N-terminal 19 residues 'GSHMVPGQKQHYVQPTAAN' correspond to a phage-display derived ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2q2h.cif.gz	67.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2q2h.ent.gz	50.4 KB	Display	PDB format
PDBx/mmJSON format	2q2h.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/q2/2q2h ftp://data.pdbj.org/pub/pdb/validation_reports/q2/2q2h	HTTPS FTP

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Related structure data

Related structure data	2q2iC 1gd7S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2z6k-1 2z7q-d 5k3l-1 4u39-8 2pi2-2 2z7s-d 3b1v-d 3p4u-1 6fx0-d 6slz-1 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, phage-display derived peptide

B: Secretion chaperone, phage-display derived peptide

hetero molecules

28.6 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)	60.528, 60.528, 115.247
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, phage-display derived peptide / AGR_C_4014p Mass: 14140.181 Da / Num. of mol.: 2 Fragment: fusion protein of a phage-display derived peptide and secretion chaperone protein 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-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.15 Å³/Da / Density % sol: 42.87 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 30% PEG 4000, 0.4 M ammonium acetate, 0.1 M sodium citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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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: Oct 27, 2006 / 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: 1.65→23.86 Å / Num. all: 25681 / Num. obs: 25681 / % possible obs: 89.4 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 5.71 % / R_merge(I) obs: 0.039 / Χ²: 0.99 / Net I/σ(I): 30 / Scaling rejects: 1109
Reflection shell	Resolution: 1.65→1.71 Å / Redundancy: 4.47 % / R_merge(I) obs: 0.162 / Mean I/σ(I) obs: 8.6 / Num. measured all: 6400 / Num. unique all: 1427 / Χ²: 1.16 / % possible all: 49.7

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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: 1.65→23.86 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.953 / SU B: 2.156 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.173	1301	5.1 %	RANDOM
R_work	0.16	-	-	-
all	0.161	25680	-	-
obs	0.161	25680	89.38 %	-

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: 8.236 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	-0.01 Å²	0 Å²
2-	-	-0.01 Å²	0 Å²
3-	-	-	0.02 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→23.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1696	0	21	307	2024

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1749
X-RAY DIFFRACTION	r_angle_refined_deg	1.183	1.993	2375
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.282	5	221
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.742	24.203	69
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.237	15	282
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.172	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	271
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1331
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	755
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	1200
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.096	0.2	248
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.181	0.2	51
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.073	0.2	25
X-RAY DIFFRACTION	r_mcbond_it	0.446	1.5	1150
X-RAY DIFFRACTION	r_mcangle_it	0.693	2	1827
X-RAY DIFFRACTION	r_scbond_it	1.155	3	648
X-RAY DIFFRACTION	r_scangle_it	1.663	4.5	548

LS refinement shell

Resolution: 1.65→1.693 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.182	49	-
R_work	0.237	962	-
obs	-	1011	47.11 %

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	5.0217	2.6406	0.1544	2.5356	-0.0234	0.7195	0.0388	-0.1094	0.1101	-0.0146	-0.0199	0.1181	0.0251	-0.0591	-0.0189	0.041	-0.0001	-0.0084	0.048	0.0083	0.0415	-44.6199	-30.0461	-15.8675
2	16.2523	-0.4069	6.2521	3.7044	1.1178	5.7734	0.1141	-0.1531	-0.0431	0.0081	-0.0594	-0.1428	0.0672	-0.044	-0.0546	0.0784	0.0138	-0.0108	0.0481	-0.0042	0.0221	-25.6101	-29.9271	-9.6992
3	6.2843	5.5966	-0.2732	9.4071	6.2022	10.123	-0.042	-0.1039	-0.2389	-0.0605	0.006	-0.4741	-0.3926	0.3345	0.036	0.0501	0.0255	0.005	0.0472	0.0165	0.0627	-18.4835	-25.892	-6.8459
4	1.04	-0.9869	4.259	2.4414	-1.1636	22.9467	-0.047	-0.0734	-0.0732	-0.1451	-0.0466	-0.0999	0.267	0.1391	0.0937	0.0802	-0.0077	0.011	0.062	-0.0036	0.0249	-15.6789	-21.4948	2.3971
5	4.1553	-3.5491	-0.5436	8.6238	4.5908	3.2008	-0.087	0.1161	0.2616	-0.0561	0.0568	-0.1756	-0.1049	0.0902	0.0302	0.0429	0.0012	-0.0073	0.0495	0.0065	0.0461	-14.732	-11.4195	15.2544
6	5.2662	-3.6408	3.3373	2.7828	-2.9562	3.7	-0.2592	-0.0174	0.2513	0.1317	0.1455	-0.2367	-0.3559	-0.0698	0.1137	0.0756	0.0023	-0.0212	0.0399	-0.0009	0.0803	-23.3667	0.5126	11.1093
7	8.9031	-5.2235	-0.3477	6.5859	-3.2671	3.4352	0.1152	0.1527	-0.309	-0.156	0.1039	0.3053	0.0275	-0.3372	-0.2191	0.0635	0.0159	-0.0145	0.0736	-0.0231	0.0381	-26.7476	-3.6786	9.7357
8	8.0369	-1.7346	-1.4744	6.301	0.5982	4.1946	-0.1723	0.1006	-0.0472	-0.0432	0.0787	-0.2986	-0.0534	0.3727	0.0937	0.0322	0.007	-0.0042	0.0871	0.0167	0.0505	-9.84	-14.7038	9.6933
9	12.8397	-8.4145	-0.1311	7.4754	1.4653	2.3401	0.0465	0.2487	0.2204	-0.0022	-0.0722	-0.3094	-0.053	0.211	0.0258	0.0421	-0.0208	0.0124	0.0486	0.0033	0.0577	-11.3533	-10.9619	6.7145
10	5.9414	3.0633	-3.1556	3.7902	-0.0018	3.7085	-0.0171	0.1774	0.1638	0.0697	0.0803	0.1413	0.0849	-0.3386	-0.0632	0.0441	0.0127	0.0041	0.0604	0.0007	0.043	-28.1331	-8.587	12.1298
11	6.7454	5.7219	5.4775	6.1844	2.7673	7.1014	-0.0179	-0.1497	0.0496	0.2607	-0.1243	0.1839	0.1133	-0.0416	0.1422	0.0672	-0.0064	0.0226	0.0566	-0.0159	0.0633	-25.7177	-10.339	19.5268
12	1.5227	-0.6494	0.3856	8.0452	0.3056	2.0635	-0.0495	-0.0187	-0.0309	0.244	0.0366	0.2793	0.024	-0.0663	0.0129	0.0274	0.0015	0.0037	0.0493	0.0041	0.0464	-19.0787	-15.6452	17.2394
13	2.1043	0.2481	-2.3632	0.0475	-0.5816	7.6698	-0.0465	0.146	-0.0167	-0.1867	0.1292	0.046	0.0506	-0.1022	-0.0826	0.0817	-0.0064	-0.0002	0.0508	-0.0036	0.0349	-17.5164	-16.533	0.7268
14	0.7869	-2.671	-1.9513	13.7546	3.8457	6.4831	-0.1448	-0.0365	0.0529	-0.1549	0.2179	0.0118	0.3216	-0.0668	-0.0732	0.0741	0.0008	-0.0083	0.0425	0.0108	0.0373	-19.3144	-4.1823	-1.2781
15	0.1167	-0.3161	0.0462	5.2579	0.2226	2.3395	0.0227	-0.0068	0.0294	-0.1917	-0.0899	-0.0889	-0.046	-0.0085	0.0673	0.0381	0.0047	0.0024	0.0491	0.0095	0.0565	-17.3457	-5.5971	2.7378
16	8.3817	2.5234	-2.423	0.8858	-1.166	2.212	0.0072	0.0207	0.1302	-0.0058	-0.0317	0.1946	-0.0417	-0.0958	0.0245	0.0411	-0.0013	-0.001	0.0437	-0.0187	0.0778	-29.2769	-17.4718	8.0075
17	8.454	-1.6728	1.7425	4.1343	1.2217	2.4604	0.0344	0.1854	0.1608	0.121	-0.1286	0.3826	0.0023	-0.2783	0.0942	0.0353	-0.0051	0.014	0.065	-0.011	0.0693	-33.0002	-15.6415	11.9098
18	7.4871	-0.9116	0.4135	1.3725	0.5037	2.3185	0.126	-0.3297	-0.1637	0.065	-0.0286	-0.0792	0.115	0.0254	-0.0974	0.0729	-0.0018	-0.0034	0.0487	0.0078	0.0373	-17.3922	-27.0838	15.4378
19	9.2889	6.3046	6.9855	7.8039	6.3686	6.4467	-0.1215	0.2793	-0.2616	-0.0264	0.1441	0.1147	0.1602	0.2228	-0.0226	0.0521	0.0012	-0.0008	0.0494	-0.0005	0.0379	-13.8405	-25.4232	5.8398
20	34.8815	-0.5291	2.9789	12.9229	-0.452	4.579	0.0821	-0.2148	0.6816	-0.8399	-0.2483	0.0621	-0.4381	0.272	0.1663	0.2488	0.007	-0.0048	-0.0261	-0.023	-0.0267	-18.9729	-14.6538	-7.3714
21	23.238	19.2375	-4.4012	16.5445	-2.2016	4.318	-0.2889	-0.0948	1.0232	-0.6631	0.0684	1.2723	-0.4989	-0.4099	0.2205	0.1418	0.0559	-0.0535	0.0189	-0.0172	0.0685	-25.2152	-19.8564	-6.5991
22	3.4214	2.1792	-5.155	2.9401	-3.2712	9.4268	0.1599	0.2727	0.0049	0.1053	0.1217	0.2333	-0.4416	-0.2921	-0.2816	0.0409	-0.0044	-0.0083	0.073	-0.0051	0.0457	-31.675	-27.0015	3.5756
23	4.4185	-0.4403	-1.9215	4.5119	-4.0787	4.9168	-0.0036	0.2106	-0.2754	-0.1272	-0.3793	-0.205	0.1058	0.2485	0.3829	0.0097	0.0115	0.0238	0.0463	0.0081	0.1176	-31.2994	-42.2281	10.7257
24	30.2124	-12.1242	-1.4083	27.9874	15.2272	9.9836	0.048	0.6788	-0.8558	-0.3208	0.164	-1.0547	1.0188	0.297	-0.212	0.0627	0.0964	0.1277	0.0166	0.1089	0.2098	-23.1593	-45.2869	7.1771
25	1.5386	-0.619	0.6285	2.0241	-1.2766	2.2031	0.0189	0.1552	-0.0966	-0.0834	-0.055	0.0279	0.0153	-0.1203	0.0362	0.0302	0	0.0156	0.071	-0.0161	0.0725	-35.596	-34.2888	5.4689
26	13.8224	-3.2279	2.0627	4.6591	-2.2292	4.167	-0.031	0.2698	0.0828	-0.1271	-0.0474	0.1504	-0.1547	-0.1153	0.0784	0.045	-0.0114	-0.003	0.0684	-0.0286	0.0524	-36.9652	-34.1371	0.9749
27	12.4722	1.3433	14.3927	6.352	0.2446	16.8835	0.1623	0.8146	-0.7084	0.0988	0.1393	-0.758	0.2255	0.7426	-0.3016	0.021	0.0186	0.0228	0.0461	0.0036	0.1928	-21.3551	-40.1571	7.5206
28	15.2174	-2.4118	-2.5352	4.1262	-3.2641	4.0117	0.3455	-0.3611	-1.1795	0.1639	-0.1971	-0.6993	0.0969	-0.0512	-0.1485	0.127	-0.0881	-0.1315	-0.009	0.0864	0.1577	-20.9644	-38.9778	15.924
29	11.2114	3.2615	0.6715	10.6833	0.8917	6.2842	0.2681	-0.9417	-0.5107	0.8133	-0.4009	-0.5484	-0.0957	0.137	0.1328	0.1051	-0.0666	-0.0099	0.0831	0.0725	0.0805	-29.0072	-37.3166	16.4935
30	0.811	-0.2223	-0.8276	0.071	0.4497	5.7918	0.0696	0.0361	-0.0733	0.0248	0.029	0.0311	-0.0998	-0.0275	-0.0985	0.0647	-0.0133	-0.0109	0.044	-0.0046	0.0475	-28.398	-29.7574	1.734
31	1.0732	-2.3742	0.1645	11.2593	-4.0621	8.1871	-0.2166	-0.0239	-0.2788	-0.0348	-0.0418	0.1192	0.0681	-0.1826	0.2584	0.0342	-0.0027	0.0194	0.0517	-0.0141	0.0924	-27.0701	-42.2006	-6.5952
32	9.9381	-15.0824	-3.2443	54.6788	-5.6865	4.6004	-0.2241	0.5499	-0.491	-0.374	-0.4265	-0.1622	0.4388	-0.3177	0.6506	0.0492	-0.0446	0.0324	0.0557	-0.0759	0.0936	-29.772	-43.5381	-2.3334
33	3.7289	2.2424	1.0036	3.4328	2.4671	1.9364	-0.0424	-0.2227	-0.1879	0.0566	0.0469	-0.2382	0.0953	-0.1081	-0.0045	0.0488	0.0047	-0.0068	0.0423	0.0186	0.0776	-19.0177	-31.3095	6.6698
34	25.7524	-6.0864	1.3304	5.6323	-0.9104	2.0298	-0.0404	0.2358	-0.5535	0.2777	-0.0635	-0.6285	0.3577	0.1675	0.1039	0.0596	0.0243	-0.038	0.0415	0.0126	0.1258	-15.67	-33.2705	11.7187
35	4.2209	-0.6075	1.3674	0.6221	-0.6391	0.8089	0.1164	-0.1416	-0.0912	-0.0245	-0.1006	0.1176	-0.0162	-0.1396	-0.0158	0.061	-0.0163	-0.003	0.0481	-0.012	0.0574	-31.428	-22.2218	14.393
36	15.5639	12.0869	-4.4561	10.9704	-3.4543	5.362	-0.3436	0.5655	0.2114	-0.221	0.3013	-0.0598	-0.165	-0.1634	0.0422	0.0402	-0.002	-0.0129	0.0378	-0.0157	0.0512	-32.6723	-21.9342	4.1683

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-4 - -1
2	X-RAY DIFFRACTION	2	A	2 - 7
3	X-RAY DIFFRACTION	3	A	8 - 12
4	X-RAY DIFFRACTION	4	A	13 - 17
5	X-RAY DIFFRACTION	5	A	18 - 23
6	X-RAY DIFFRACTION	6	A	24 - 29
7	X-RAY DIFFRACTION	7	A	30 - 36
8	X-RAY DIFFRACTION	8	A	37 - 43
9	X-RAY DIFFRACTION	9	A	44 - 49
10	X-RAY DIFFRACTION	10	A	50 - 55
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