PDB-3del: The structure of CT381, the arginine binding protein from the per...

ID or keywords:

Entry

Database: PDB / ID: 3del

Title

The structure of CT381, the arginine binding protein from the periplasm Chlamydia trachomatis

Components

Arginine Binding Protein

Keywords

PROTEIN BINDING / TRANSPORT PROTEIN / Alpha and Beta protein (a/b) / periplasmic protein / arginine binding

Function / homology

Function and homology information

amino acid binding / amino acid transport / outer membrane-bounded periplasmic space / cell surface / extracellular region
Similarity search - Function

Biological species

Chlamydia trachomatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.92 Å

Authors

Petit, P. / Vuillard, L. / Spinelli, S.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Exploiting antigenic diversity for vaccine design: the Chlamydia ArtJ paradigm.
Authors: Soriani, M. / Petit, P. / Grifantini, R. / Petracca, R. / Gancitano, G. / Frigimelica, E. / Nardelli, F. / Garcia, C. / Spinelli, S. / Scarabelli, G. / Fiorucci, S. / Affentranger, R. / ...

History

Deposition	Jun 10, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 16, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3del.cif.gz	213.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3del.ent.gz	169.4 KB	Display	PDB format
PDBx/mmJSON format	3del.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3del_validation.pdf.gz	452 KB	Display	wwPDB validaton report
Full document	3del_full_validation.pdf.gz	460.5 KB	Display
Data in XML	3del_validation.xml.gz	45.8 KB	Display
Data in CIF	3del_validation.cif.gz	71 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/de/3del ftp://data.pdbj.org/pub/pdb/validation_reports/de/3del	HTTPS FTP

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Related structure data

Related structure data	3n26C 1hsl C: citing same article (ref.)
Similar structure data	6swb-d 6swf-d 3tfm-d 3mlq-3 1avv-1 3aq8-d 3v8r-d 7jz5-d 6ifb-d 3p13-2 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

3n26C

1hsl

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: Arginine Binding Protein

C: Arginine Binding Protein

D: Arginine Binding Protein

F: Arginine Binding Protein

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

1

B: Arginine Binding Protein

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

2

C: Arginine Binding Protein

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

3

D: Arginine Binding Protein

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

4

F: Arginine Binding Protein

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

Unit cell

Length a, b, c (Å)	40.072, 121.875, 170.097
Angle α, β, γ (deg.)	90.00, 95.38, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Arginine Binding Protein Mass: 27128.012 Da / Num. of mol.: 4 / Fragment: CT381 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: artJ, CT_381 / Plasmid: pET21b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O84385
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1284 / 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: 3.81 Å³/Da / Density % sol: 67.72 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Sodium Formate 0.5M-4M, Tris Base 100mM, pH 6.8-8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97995 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2008
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97995 Å / Relative weight: 1
Reflection	Resolution: 1.92→55 Å / Num. obs: 123164 / % possible obs: 99.5 % / Observed criterion σ(I): 2.1 / Redundancy: 4.1 % / B_iso Wilson estimate: 21.2 Å² / R_merge(I) obs: 0.086 / R_sym value: 0.086 / Net I/σ(I): 13.8
Reflection shell	Resolution: 1.92→2.02 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / Num. unique all: 17384 / R_sym value: 0.48 / % possible all: 96.6

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC	Quantum	data collection
MOSFLM		data reduction
SCALA		data scaling
SHELXS		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.92→30 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.926 / SU B: 5.254 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.12 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2133	1237	1 %	RANDOM
R_work	0.19584	-	-	-
obs	0.196	121860	99.48 %	-
all	-	123129	-	-

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: 5.549 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.43 Å²	0 Å²	0.22 Å²
2-	-	0.44 Å²	0 Å²
3-	-	-	0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.92→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7372	0	0	1284	8656

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	7593
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.127	1.966	10318
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.538	5	944
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.252	24.519	343
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.211	15	1345
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.834	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	1186
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5676
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.184	0.2	3389
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.295	0.2	5155
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	964
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.21	0.2	113
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.149	0.2	55
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.339	1.5	4834
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.496	2	7568
X-RAY DIFFRACTION	r_scbond_it	1.199	3	3122
X-RAY DIFFRACTION	r_scangle_it	2.047	4.5	2740
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.92→1.97 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	95	-
R_work	0.299	8432	-
obs	-	-	94.14 %

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	1.1793	-0.6814	-0.4373	3.5507	-0.0611	0.6694	-0.0588	-0.2233	-0.159	0.7255	0.0121	0.1918	0.0547	-0.0491	0.0467	0.3228	-0.0073	0.1013	-0.0402	-0.0154	-0.1336	13.88	0.404	173.63
2	0.3073	-0.0228	0.4991	3.8886	-0.3872	3.6792	0.0755	-0.0349	-0.1061	0.5855	-0.0606	0.5833	-0.0701	-0.2864	-0.0149	0.2333	0.0129	0.134	-0.0283	-0.0729	-0.0514	8.889	9.031	168.417
3	0.5979	0.1155	-0.0865	0.0666	0.4969	5.9649	0.0089	0.0094	0.1075	0.054	-0.1066	0.1476	-0.4227	0.0176	0.0978	0.2115	0.0007	0.0126	-0.0877	-0.0487	-0.0253	14.57	10.547	155.762
4	5.8453	-0.9948	2.0619	4.1378	1.1308	1.4841	-0.1825	0.588	0.4024	-0.4241	0.1111	0.1019	-0.1492	-0.1881	0.0714	0.0831	0.023	-0.0775	0.0178	0.0405	-0.0121	8.957	6.412	130.491
5	1.4171	-0.3935	-0.8346	2.3111	0.8426	2.2358	-0.011	0.0603	-0.0551	0.0548	-0.1021	0.2013	-0.0837	-0.1983	0.1131	0.0473	-0.0031	-0.0021	0.0033	-0.022	-0.0087	10.864	-2.489	140.267
6	0.7621	-0.5468	-1.1872	1.4749	1.5336	4.3095	0.0094	-0.0288	0.1018	0.0501	-0.0536	0.0292	-0.3073	0.1108	0.0442	0.1151	-0.0002	0.0012	-0.0735	-0.036	-0.024	16.723	7.959	147.118
7	1.6014	-2.2573	-0.2529	5.7915	1.4146	1.6959	-0.0643	-0.1925	0.1768	0.3917	0.1127	-0.3998	-0.1308	0.1792	-0.0484	0.2737	-0.0261	0.0043	-0.0996	-0.0352	-0.1006	24.297	8.347	169.055
8	8.3657	-1.7976	0.6108	6.8737	0.3392	10.7891	0.2131	0.3669	-0.4304	0.259	-0.3296	0.3622	0.3366	-0.1775	0.1164	0.1784	-0.0313	0.0609	-0.1379	-0.0464	-0.0872	14.428	-1.912	156.455
9	0.5343	0.5256	0.3814	3.2791	0.2018	0.8936	-0.0438	0.1121	0.1067	-0.6071	-0.0183	0.0373	-0.1035	-0.0018	0.0621	0.2643	0.0074	0.0034	-0.0626	-0.0255	-0.103	22.442	-14.794	78.583
10	0.9202	-0.1213	-0.005	2.6056	-0.5727	2.9554	-0.0266	0.0681	-0.0434	-0.4039	-0.0395	0.1535	0.0669	-0.1743	0.0661	0.2116	0.0164	-0.0025	-0.0596	-0.0728	-0.042	18.166	-23.937	85.795
11	1.421	-0.5576	-3.2895	1.3168	3.7187	15.2982	-0.0876	-0.1915	-0.3041	-0.0128	0.0753	-0.0452	0.5727	0.4811	0.0123	0.0972	0.0251	0.0249	-0.0544	-0.0248	0.0122	18.776	-22.252	108.358
12	12.2381	1.7621	1.5456	8.2799	1.6244	1.6859	-0.0106	-1.3754	-1.5709	0.6345	0.1481	0.2058	0.1723	-0.4694	-0.1375	0.0317	-0.045	0.0818	0.1102	0.1252	0.0805	10.254	-21.517	121.207
13	1.9002	0.0291	0.4896	2.0462	0.5698	2.0192	0.0028	-0.0658	-0.0483	-0.0965	-0.0797	0.1182	-0.0192	-0.1532	0.0769	0.0492	0.0158	0.0088	-0.025	-0.0167	-0.0127	12.684	-11.414	111.645
14	0.2102	0.1628	0.2357	1.1191	1.5949	4.7394	-0.0509	-0.0249	-0.1228	-0.0388	-0.0582	-0.0092	0.2684	0.072	0.1091	0.0896	0.0089	0.0061	-0.0636	-0.028	0.0102	20.344	-21.622	105.244
15	1.1015	1.7706	0.4994	5.5131	1.3092	1.4787	-0.0081	0.1408	-0.1295	-0.1479	0.0191	-0.4414	0.141	0.1566	-0.011	0.1891	0.0372	0.0651	-0.0905	-0.0287	-0.0457	31.947	-21.9	85.553
16	9.8818	8.6668	5.3842	12.9111	6.6489	16.6161	0.0273	-0.1347	0.2717	-0.1757	-0.1378	0.1932	-0.4513	-0.1823	0.1105	0.1413	0.0564	0.0205	-0.1287	-0.0384	-0.0843	19.224	-11.826	95.66
17	0.5737	-0.4663	0.4646	3.414	0.0333	1.3427	-0.0145	-0.148	0.0716	0.6002	-0.062	-0.0154	-0.1234	0.0236	0.0765	0.273	-0.0257	0.0305	-0.0533	0.0319	-0.1224	-12.042	-20.755	173.417
18	1.9413	-0.4487	-0.313	2.7509	-0.4557	4.3096	0.0345	-0.0428	-0.0903	0.2126	-0.1343	-0.0819	0.1833	0.1885	0.0998	0.1936	-0.0306	0.0171	-0.0696	0.0702	-0.0653	-7.998	-28.871	164.732
19	1.5493	0.7232	-1.25	3.2484	-3.0897	9.0101	0.0755	0.166	-0.1776	0.0503	0.0092	0.1269	0.274	0.025	-0.0847	0.0588	-0.0089	0.0082	-0.0502	0.0173	-0.0012	-8.253	-23.403	140.367
20	5.5043	1.1342	-2.1961	7.0799	2.998	5.5097	-0.123	0.8652	-0.3045	-0.3652	-0.1978	0.0195	0.1613	0.2179	0.3207	0.0239	0.0802	0.0368	0.1367	-0.0094	0.0223	1.42	-20.392	131.489
21	1.5276	0.4096	0.6911	2.0535	-0.7081	2.6689	-0.0155	0.0342	-0.0329	0.1054	-0.0863	-0.1245	-0.0503	0.1741	0.1018	0.0399	-0.0197	-0.0047	-0.0159	0.0265	-0.0086	-3.687	-13.147	141.756
22	0.4604	-0.4561	0.8071	1.6399	-2.1007	4.7825	-0.0099	0.0209	-0.1416	-0.0004	-0.0623	0.0082	0.2884	-0.1528	0.0723	0.0996	-0.0308	0.0169	-0.0775	0.0257	-0.0088	-10.528	-24.007	145.417
23	1.6429	-2.1871	0.782	6.7232	-2.1833	2.1031	0.0864	-0.0706	-0.25	0.1544	0.0374	0.6752	0.1545	-0.1462	-0.1238	0.1707	-0.0375	0.0686	-0.0987	0.0238	-0.0457	-21.041	-27.686	166.052
24	14.3821	-8.667	4.9041	12.899	-4.9553	11.362	0.1507	-0.0191	0.243	0.2602	-0.2548	-0.0261	-0.8247	0.1459	0.1041	0.2011	-0.047	0.0225	-0.104	0.0494	-0.1105	-9.224	-16.032	156.613
25	0.8845	0.8868	-0.6094	3.8922	0.0892	0.7464	-0.0646	0.0774	-0.1144	-0.5714	-0.019	-0.139	0.0021	0.0051	0.0836	0.2576	0.0133	0.0544	-0.0738	0.021	-0.1004	36.484	6.555	81.28
26	1.1319	0.3921	-0.2128	4.2854	0.0107	3.4001	0.0556	-0.0218	-0.0638	-0.2035	-0.137	-0.1869	-0.0972	0.0975	0.0814	0.1772	-0.0112	0.0192	-0.077	0.0585	-0.0586	39.029	15.122	90.085
27	1.4986	0.4269	-1.761	6.3287	-6.2734	13.0424	0.1277	-0.2208	0.1434	0.2399	0.1568	0.1464	-0.6578	-0.0966	-0.2844	0.0881	-0.0048	-0.0162	-0.0486	0.0073	-0.0168	34.108	9.356	116.448
28	3.0706	-0.9466	1.366	8.156	6.9116	9.7877	-0.1299	-0.148	-0.0241	0.3169	-0.1413	-0.1013	-0.3032	0.0404	0.2713	0.0595	-0.0354	-0.0616	-0.0104	0.0009	-0.0066	43.384	7.494	123.9
29	1.1898	-0.0574	-0.3622	2.1252	-0.6008	2.3132	-0.0135	-0.0559	-0.0482	-0.0586	-0.1097	-0.1616	-0.1304	0.1904	0.1232	0.046	-0.012	-0.0024	-0.0048	0.0311	-0.0102	38.326	-0.166	113.63
30	0.4889	0.7182	-1	1.7234	-1.8167	3.8938	0.0454	-0.0208	0.0879	0.1007	-0.0855	-0.0606	-0.4408	-0.0545	0.0401	0.1141	-0.0011	-0.003	-0.0736	0.0312	-0.0095	33.515	10.88	108.371
31	2.458	3.0163	-0.535	6.1212	-1.0863	1.226	0.0238	0.0964	0.3272	-0.2037	0.0586	0.5773	-0.1306	-0.1254	-0.0824	0.1926	0.0224	-0.0088	-0.1066	0.0094	-0.0435	26.064	13.965	86.326
32	8.2765	3.6411	-2.046	7.4974	-3.1271	8.8813	0.0421	-0.3241	-0.3718	-0.0651	-0.2672	-0.111	0.479	0.2731	0.2251	0.2258	0.0268	0.0475	-0.1217	0.0422	-0.0774	35.485	2.116	97.936

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	B	A	34 - 91	11 - 68
2	X-RAY DIFFRACTION	2	B	A	92 - 108	69 - 85
3	X-RAY DIFFRACTION	3	B	A	109 - 127	86 - 104
4	X-RAY DIFFRACTION	4	B	A	128 - 142	105 - 119
5	X-RAY DIFFRACTION	5	B	A	143 - 188	120 - 165
6	X-RAY DIFFRACTION	6	B	A	189 - 224	166 - 201
7	X-RAY DIFFRACTION	7	B	A	225 - 254	202 - 231
8	X-RAY DIFFRACTION	8	B	A	255 - 265	232 - 242
9	X-RAY DIFFRACTION	9	C	B	34 - 92	11 - 69
10	X-RAY DIFFRACTION	10	C	B	93 - 118	70 - 95
11	X-RAY DIFFRACTION	11	C	B	119 - 128	96 - 105
12	X-RAY DIFFRACTION	12	C	B	129 - 139	106 - 116
13	X-RAY DIFFRACTION	13	C	B	140 - 188	117 - 165
14	X-RAY DIFFRACTION	14	C	B	189 - 224	166 - 201
15	X-RAY DIFFRACTION	15	C	B	225 - 255	202 - 232
16	X-RAY DIFFRACTION	16	C	B	256 - 265	233 - 242
17	X-RAY DIFFRACTION	17	D	C	34 - 92	11 - 69
18	X-RAY DIFFRACTION	18	D	C	93 - 119	70 - 96
19	X-RAY DIFFRACTION	19	D	C	120 - 129	97 - 106
20	X-RAY DIFFRACTION	20	D	C	130 - 143	107 - 120
21	X-RAY DIFFRACTION	21	D	C	144 - 188	121 - 165
22	X-RAY DIFFRACTION	22	D	C	189 - 223	166 - 200
23	X-RAY DIFFRACTION	23	D	C	224 - 255	201 - 232
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26	X-RAY DIFFRACTION	26	F	D	92 - 119	69 - 96
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28	X-RAY DIFFRACTION	28	F	D	132 - 142	109 - 119
29	X-RAY DIFFRACTION	29	F	D	143 - 191	120 - 168
30	X-RAY DIFFRACTION	30	F	D	192 - 224	169 - 201
31	X-RAY DIFFRACTION	31	F	D	225 - 254	202 - 231
32	X-RAY DIFFRACTION	32	F	D	255 - 265	232 - 242

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