PDB-6uxc: 1.65A resolution structure of the hypothetical protein CT253 from...

ID or keywords:

Entry

Database: PDB / ID: 6uxc

Title

1.65A resolution structure of the hypothetical protein CT253 from Chlamydia trachomatis

Components

CT253

Keywords

UNKNOWN FUNCTION / CT253 / Chlamydia trachomatis

Function / homology

Putative lipoprotein

Function and homology information

Biological species

Chlamydia trachomatis serovar L2 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD /

molecular replacement / Resolution: 1.65 Å

Authors

Barta, M.L. / Lovell, S. / Battaile, K.P. / Hefty, P.S.

Funding support

United States, 1items

Citation

Journal: To be published
Title: 1.65A resolution structure of the hypothetical protein CT253 from Chlamydia trachomatis
Authors: Barta, M.L. / Lovell, S. / Battaile, K.P. / Hefty, P.S.

History

Deposition	Nov 7, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 11, 2020	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6uxc.cif.gz	149.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6uxc.ent.gz	122 KB	Display	PDB format
PDBx/mmJSON format	6uxc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6uxc_validation.pdf.gz	439.4 KB	Display	wwPDB validaton report
Full document	6uxc_full_validation.pdf.gz	440.2 KB	Display
Data in XML	6uxc_validation.xml.gz	16.6 KB	Display
Data in CIF	6uxc_validation.cif.gz	23.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ux/6uxc ftp://data.pdbj.org/pub/pdb/validation_reports/ux/6uxc	HTTPS FTP

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Related structure data

Similar structure data	4w56-d 210l-d 4w52-d 2w2s-d 111l-d 5jgz-d 4w53-d 7lzm-d 4w54-d 4w59-d 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CT253

B: CT253

hetero molecules

42.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CT253

hetero molecules

defined by author
Evidence: gel filtration
21.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: CT253

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.187, 80.187, 114.841
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	B-513- HOH

#1: Protein	CT253 Mass: 21354.154 Da / Num. of mol.: 2 / Fragment: S26-S215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B) (bacteria) Strain: 434/Bu / ATCC VR-902B / Gene: CTL0505 / Plasmid: pTBSG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3MBU8
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.71 % / Mosaicity: 0.13 °
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2 M sodium formate, 0.1M Tris

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 17-ID / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2013

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.65→44.25 Å / Num. obs: 51872 / % possible obs: 99.7 % / Redundancy: 9.4 % / CC_1/2: 1 / R_merge(I) obs: 0.049 / Net I/σ(I): 20.2 / Num. measured all: 487014 / Scaling rejects: 4752

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	Net I/σ(I) obs	% possible all
1.65-1.68	9.8	1.525	24989	2562	0.647	1.6	100
9.04-44.25	9.1	0.024	3426	378	0.999	68.5	99.4

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Phasing

Phasing

Method
SAD
molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	6.35 Å	34.72 Å
Translation	6.35 Å	34.72 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3678	refinement
XDS		data reduction
Aimless	0.7.4	data scaling
PHASER	2.5.6	phasing
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 1.65→34.72 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 19.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2039	2426	4.83 %
R_work	0.1713	47832	-
obs	0.1729	50258	96.66 %

Solvent computation

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

Displacement parameters

B_iso max: 124.49 Å² / B_iso mean: 37.3254 Å² / B_iso min: 19.25 Å²

Refinement step

Cycle: final / Resolution: 1.65→34.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2596	0	2	265	2863
B_iso mean	-	-	25.99	42.85	-
Num. residues	-	-	-	-	335

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 17

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.65-1.68	0.2818	176	0.2693	2822	2998	99
1.68-1.72	0.2792	137	0.2386	2822	2959	98
1.72-1.76	0.2363	137	0.2199	2830	2967	98
1.76-1.8	0.2342	152	0.2118	2799	2951	98
1.8-1.85	0.2553	136	0.2028	2810	2946	97
1.85-1.91	0.2463	161	0.19	2773	2934	97
1.91-1.97	0.2047	112	0.1733	2821	2933	97
1.97-2.04	0.199	146	0.1652	2888	3034	100
2.04-2.12	0.1916	155	0.1583	2888	3043	100
2.12-2.22	0.1978	127	0.1514	2896	3023	100
2.22-2.33	0.1858	125	0.1605	2752	2877	94
2.33-2.48	0.2158	131	0.1674	2612	2743	90
2.48-2.67	0.2065	145	0.1764	2748	2893	94
2.67-2.94	0.2151	160	0.1822	2910	3070	100
2.94-3.37	0.2245	132	0.1824	2716	2848	92
3.37-4.24	0.176	138	0.1478	2920	3058	98
4.24-34.72	0.1927	156	0.1708	2825	2981	91

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	1.1999	-0.3568	-0.1657	0.5856	1.0694	2.1638	0.1054	0.0897	0.1392	-0.2045	-0.0096	-0.1653	-0.3828	0.1865	-0.0483	0.3172	-0.0201	-0.0009	0.2351	0.0258	0.2764	-12.7347	23.5033	-8.3852
2	1.9899	1.0721	-1.5265	2.9456	-1.8502	4.1864	-0.1818	0.0888	-0.2519	-0.3508	0.1098	-0.2119	0.5956	-0.1728	0.0768	0.3019	-0.0173	0.0189	0.2115	-0.0154	0.2836	-16.3599	13.7332	-8.0099
3	2.2949	0.8066	-0.0758	1.3399	0.3403	0.6997	0.1466	-0.2635	0.1974	0.1665	-0.1253	0.0624	-0.008	0.0363	-0.0269	0.3079	-0.0414	-0.009	0.2761	0.0032	0.278	-18.2006	25.0026	6.2345
4	1.1361	-0.0365	-0.1863	1.1406	-0.1787	3.2431	0.1014	-0.0507	-0.0305	-0.141	-0.0756	-0.3327	-0.052	0.567	-0.0152	0.2688	-0.0012	0.0283	0.2715	0.0282	0.3523	-4.2912	21.0796	-5.7169
5	3.9077	3.029	0.2427	9.2159	-0.6851	5.4709	0.0235	-1.0547	-0.0824	0.3629	-0.0571	-0.07	0.3734	0.4742	0.1132	0.3991	-0.054	-0.0298	0.4538	0.0815	0.2866	-17.7035	17.4973	14.8398
6	1.1756	0.3896	-0.6885	1.308	-1.4275	4.1808	-0.1222	0.0276	-0.2282	-0.3805	0.0188	-0.3196	0.5964	0.1407	0.092	0.3791	-0.0225	0.0838	0.2247	-0.024	0.362	-5.7461	17.2014	-16.4703
7	2.4357	0.6672	-1.8851	3.0449	-2.5303	6.2791	-0.1211	-0.1265	-0.2871	-0.13	-0.0709	-0.4447	0.4154	0.2923	0.1716	0.3295	0.0642	0.0062	0.2152	0.0053	0.4078	-6.9037	11.4326	-6.7396
8	6.0048	-0.194	2.3888	2.3109	-0.8387	3.1797	0.0703	0.0125	-0.1052	0.1695	0.0689	-0.126	-0.2133	0.8308	-0.2437	0.2562	-0.0459	0.02	0.3627	-0.0248	0.186	-4.2435	46.4352	10.4594
9	5.794	-1.5905	4.8777	5.6308	-1.055	4.1252	0.0296	-1.2493	0.2396	0.9637	-0.3825	-0.7397	-0.2928	0.3848	0.3841	0.3967	-0.0766	-0.0421	0.4756	0.0012	0.3831	11.4766	54.5112	14.0507
10	2.5138	-0.4599	1.0374	1.5262	-0.1704	0.8595	-0.0661	-0.2065	0.0613	0.0538	0.045	0.1122	-0.0492	-0.0079	0.0375	0.2536	-0.0194	0.0018	0.2458	0.0078	0.2149	-7.8611	47.9204	7.8103
11	4.8029	0.3392	-2.5619	4.6709	-2.8093	8.7694	-0.0329	-0.5221	-0.0287	0.5433	0.4418	0.4235	0.0602	-0.6183	-0.4612	0.287	0.0168	0.0186	0.3578	0.0527	0.3147	-20.7378	45.5346	10.1016
12	5.517	0.7866	0.8551	1.6702	-0.6191	1.4084	0.0659	-0.4159	0.0861	-0.0225	-0.2017	-0.2839	0.0919	0.1874	0.0792	0.2374	-0.0151	0.0081	0.3139	0.0443	0.2215	1.3918	42.2232	10.6829
13	4.8757	-4.1667	-4.0885	5.9813	4.2591	3.7338	-0.1092	-0.325	-0.2176	0.2159	0.534	0.2939	1.0215	0.1466	-0.3344	0.5665	0.1438	0.0358	0.7394	0.1535	0.7535	23.4452	36.8909	7.942
14	1.4883	-0.4428	-0.5476	0.9951	-0.1131	1.5163	0.0546	-0.6955	-0.3435	0.0672	-0.0169	0.1471	0.1026	-0.1381	-0.0204	0.261	-0.0474	-0.0033	0.2614	0.047	0.2642	-7.4211	38.7379	7.9999
15	2.6904	0.9523	0.9136	1.6544	0.0719	0.7177	-0.168	0.317	0.1153	-0.2408	0.0651	-0.1185	-0.0522	0.1639	0.0833	0.2698	-0.0301	0.0048	0.3252	0.0622	0.2959	9.9683	47.4037	4.6221
16	7.1233	2.2183	2.0928	2.6141	0.6214	2.4981	-0.1428	0.2387	-0.0637	-0.2399	0.0894	-0.0798	0.0495	0.2583	0.1095	0.2286	-0.007	0.0155	0.213	0.0155	0.1646	1.2802	42.187	-0.402

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 43 through 65 )	A	43 - 65
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 66 through 86 )	A	66 - 86
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 87 through 118 )	A	87 - 118
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 119 through 149 )	A	119 - 149
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 150 through 155 )	A	150 - 155
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 156 through 189 )	A	156 - 189
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 190 through 213 )	A	190 - 213
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 42 through 58 )	B	42 - 58
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 59 through 65 )	B	59 - 65
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 66 through 107 )	B	66 - 107
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 108 through 118 )	B	108 - 118
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 119 through 130 )	B	119 - 130
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 131 through 137 )	B	131 - 137
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 138 through 155 )	B	138 - 155
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 156 through 189 )	B	156 - 189
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 190 through 213 )	B	190 - 213

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