PDB-4qar: 1.45 A resolution structure of CT263 (MTAN) from Chlamydia tracho...

ID or keywords:

Entry

Database: PDB / ID: 4qar

Title

1.45 A resolution structure of CT263 (MTAN) from Chlamydia trachomatis bound to Adenine

Components

CT263

Keywords

HYDROLASE / Chlamydia / quinones / nucleosidase / futalosine pathway / product-bound

Function / homology

Function and homology information

nucleoside metabolic process / catalytic activity
Similarity search - Function

Biological species

Chlamydia trachomatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

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

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Structural and Biochemical Characterization of Chlamydia trachomatis Hypothetical Protein CT263 Supports That Menaquinone Synthesis Occurs through the Futalosine Pathway.
Authors: Barta, M.L. / Thomas, K. / Yuan, H. / Lovell, S. / Battaile, K.P. / Schramm, V.L. / Hefty, P.S.

History

Deposition	May 5, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 17, 2014	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	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 / 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
Revision 1.4	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4qar.cif.gz	168.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4qar.ent.gz	135.1 KB	Display	PDB format
PDBx/mmJSON format	4qar.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4qar_validation.pdf.gz	450 KB	Display	wwPDB validaton report
Full document	4qar_full_validation.pdf.gz	451.9 KB	Display
Data in XML	4qar_validation.xml.gz	18.3 KB	Display
Data in CIF	4qar_validation.cif.gz	26.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qa/4qar ftp://data.pdbj.org/pub/pdb/validation_reports/qa/4qar	HTTPS FTP

-
Related structure data

Related structure data	4qaqC 4qasC 4qatC 4qfbC C: citing same article (ref.)
Similar structure data	5yl8-d 4qas-1 1ces-d 1apn-d 5jd3-12 5jd3-9 5bn1-d 1ens-d 6r4t-2 1zuo-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1)

Deposited unit

A: CT263

B: CT263

hetero molecules

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

1

A: CT263

hetero molecules

B: CT263

hetero molecules

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

2

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	65.640, 104.493, 58.211
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	CT263 Mass: 22351.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: 434/Bu / ATCC VR-902B / Gene: CTL0515 / Plasmid: pT7HmT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0B7H9, UniProt: A0A0H3MBV9*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ADE / ADENINE Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₅N₅
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.91 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 200 mM ammonium sulfate, 100 mM sodium acetate trihydrate (pH 4.6) and 30% (w/v) PEG 2K MME, vapor diffusion, sitting drop, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2013
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.45→65.64 Å / Num. all: 71624 / Num. obs: 71123 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / B_iso Wilson estimate: 13.41 Å² / R_merge(I) obs: 0.076 / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.45→1.47 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3459 / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
Aimless		data scaling
PHENIX	1.8.4_1496	refinement
PDB_EXTRACT	3.14	data extraction
JDirector		data collection
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: apo-CT263

Resolution: 1.45→33.453 Å / FOM work R set: 0.8498 / SU ML: 0.16 / σ(F): 1.33 / Phase error: 21.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2168	3573	5.06 %	RANDOM
R_work	0.1869	-	-	-
all	0.1884	71660	-	-
obs	0.1884	70635	98.57 %	-

Solvent computation

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

Displacement parameters

B_iso max: 88.97 Å² / B_iso mean: 20.88 Å² / B_iso min: 6.41 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→33.453 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2939	0	15	303	3257

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3083
X-RAY DIFFRACTION	f_angle_d	1.059	4223
X-RAY DIFFRACTION	f_chiral_restr	0.079	497
X-RAY DIFFRACTION	f_plane_restr	0.008	531
X-RAY DIFFRACTION	f_dihedral_angle_d	11.83	1116

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.45-1.4691	0.4593	140	0.402	2507	2647	98
1.4691-1.4892	0.4927	145	0.4541	2488	2633	97
1.4892-1.5105	0.2942	133	0.2836	2548	2681	100
1.5105-1.533	0.5246	127	0.4431	2540	2667	97
1.533-1.557	0.2632	141	0.2384	2543	2684	99
1.557-1.5825	0.2057	141	0.1999	2581	2722	100
1.5825-1.6098	0.2404	133	0.1849	2593	2726	100
1.6098-1.6391	0.2239	137	0.1836	2579	2716	100
1.6391-1.6706	0.2098	130	0.1854	2608	2738	100
1.6706-1.7047	0.218	146	0.1837	2575	2721	100
1.7047-1.7418	0.2155	140	0.1955	2575	2715	99
1.7418-1.7823	0.2046	158	0.1696	2591	2749	100
1.7823-1.8269	0.2014	136	0.167	2615	2751	100
1.8269-1.8762	0.1692	150	0.1683	2581	2731	100
1.8762-1.9315	0.4077	118	0.2782	2385	2503	91
1.9315-1.9938	0.2149	123	0.1872	2582	2705	98
1.9938-2.065	0.2138	126	0.1734	2574	2700	99
2.065-2.1477	0.2122	124	0.1906	2500	2624	96
2.1477-2.2454	0.192	125	0.1725	2590	2715	98
2.2454-2.3638	0.1901	133	0.1776	2484	2617	95
2.3638-2.5118	0.1986	130	0.1622	2642	2772	100
2.5118-2.7057	0.2003	150	0.1658	2609	2759	100
2.7057-2.9778	0.2073	138	0.1667	2659	2797	100
2.9778-3.4084	0.1934	148	0.1623	2672	2820	100
3.4084-4.2928	0.168	147	0.1545	2615	2762	98
4.2928-33.4623	0.1952	154	0.1676	2826	2980	99

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	2.7281	-0.4384	-0.2416	1.8303	-0.3598	1.6433	-0.0946	0.032	-0.0169	-0.256	0.0494	0.1258	0.1271	0.0022	0.0772	0.1895	-0.0449	-0.035	0.0611	0.019	0.0411	98.326	134.613	55.268
2	1.6095	2.9767	-0.0829	5.5695	-0.4738	3.0905	-0.4298	0.2483	-0.0779	-0.5713	0.1994	0.0948	0.0942	-0.5478	0.1825	0.2277	-0.0808	-0.0176	0.1915	-0.0097	0.1265	91.34	133.721	47.349
3	4.4678	-0.4621	-1.2612	3.3304	0.4424	4.1978	-0.1359	0.2689	-0.0018	-0.5256	0.0625	-0.1877	0.2285	-0.0144	0.0805	0.2576	-0.0562	-0.0135	0.1194	-0.0045	0.1048	98.848	131.595	47.505
4	1.4531	0.2467	0.0606	1.9659	0.9326	2.479	-0.0606	-0.0129	-0.1088	-0.0248	-0.0428	0.3006	0.2518	-0.3486	0.0261	0.173	-0.0347	-0.008	0.0814	0.0098	0.1032	95.739	130.683	64.716
5	1.8092	1.5557	-0.9689	1.1924	-0.7209	0.6816	0.0643	-0.2295	-0.0641	0.0292	-0.2122	0.0688	0.0737	0.0827	0.1258	0.1564	-0.0085	0.0125	0.0815	-0.0091	0.0918	101.365	124.181	74.662
6	7.6854	0.6563	-1.161	3.6437	1.3591	1.3993	-0.2399	0.0941	-0.1934	-0.2925	0.2069	-0.1123	0.1414	0.1211	0.0366	0.1251	0.006	0.0042	0.0528	0.0046	0.0517	109.314	128.668	67.046
7	1.8128	2.3979	0.2712	3.4332	1.2259	2.7265	0.047	-0.4727	-0.1773	0.8846	-0.2646	0.3182	0.4676	-0.0838	0.115	0.3059	0.0035	0.0463	0.2307	0.0229	0.1115	99.247	132.655	81.395
8	1.5769	0.2589	0.0745	2.2046	-0.035	1.9814	-0.042	-0.1187	-0.1354	-0.0379	0.044	0.0789	0.1059	-0.1657	0.0311	0.1113	0.0014	0.0053	0.0846	0.018	0.0571	98.633	132.318	69.168
9	4.0309	-1.6688	-1.2479	4.3913	1.8595	4.8183	-0.0643	0.4728	-0.3287	-0.406	0.1518	-0.3891	-0.0416	0.3739	-0.0319	0.2066	-0.0675	0.0023	0.1402	0.0079	0.017	106.286	137.988	56.069
10	6.5426	0.017	-3.8173	5.3191	0.0859	2.5967	0.1881	0.5503	0.1002	-0.1995	0.1476	-0.1874	0.1072	-0.2806	-0.1168	0.0941	0.0162	-0.0246	0.1078	-0.0098	0.064	79.769	104.806	66.376
11	2.8119	-0.2969	0.7697	3.0343	-0.3905	2.925	0.0939	0.082	-0.1358	-0.1085	-0.0873	0.0069	0.2192	0.0056	0.0067	0.0964	0.0066	0.0058	0.0716	0.0044	0.0392	72.395	104.937	66.035
12	4.5818	0.2288	-2.7753	4.5544	-0.0104	2.6214	-0.2702	-0.2462	-0.7581	0.1361	-0.0683	0.0658	0.8474	0.1381	0.1817	0.2289	-0.0071	-0.0106	0.1277	0.0099	0.1984	81.382	95.126	72.272
13	2.0531	-0.324	-0.7145	1.888	0.927	2.6572	0.032	-0.3072	0.1156	0.1215	0.0613	-0.2115	-0.078	0.1205	-0.036	0.1046	0.0129	-0.0158	0.082	-0.0279	0.0704	84.91	112.73	81.004
14	2.8197	0.3182	-0.7005	3.1903	-0.2848	3.8107	-0.0343	-0.173	0.0223	0.0797	0.0548	-0.2689	-0.0004	0.425	-0.0107	0.0777	0.0166	-0.0138	0.0963	-0.0295	0.1006	90.686	110.835	78.139
15	2.2271	-0.1649	-0.5274	4.5367	2.7853	5.1104	-0.112	-0.4899	-0.0969	0.6221	-0.0363	0.0414	0.4741	0.0236	0.0701	0.1628	0.0233	-0.022	0.143	0.008	0.0771	85.405	104.279	84.913
16	1.4809	-0.7326	-1.2659	1.8298	1.6396	2.2407	0.0349	-0.1934	0.071	0.0707	0.1108	-0.235	0.0121	0.0863	-0.1039	0.1326	0.0231	-0.0037	0.0914	-0.0125	0.0669	81.945	111.019	81.992
17	2.8813	0.1434	-0.7746	2.0641	0.8465	2.5281	-0.0075	0.1904	0.0958	-0.1694	0.0364	-0.1027	-0.1503	-0.1766	0.042	0.1677	0.0135	-0.0054	0.0596	-0.0114	0.0545	75.223	115.995	74.434
18	3.7709	2.7259	5.4854	3.3142	4.8768	8.5979	0.185	0.2732	-0.1297	-0.0518	-0.121	0.1658	0.3768	0.4686	-0.0212	0.2762	-0.0014	0.061	0.2482	-0.0511	0.4422	78.72	108.532	87.607

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 1:20 )	A	1 - 20
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 21:30 )	A	21 - 30
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 31:44 )	A	31 - 44
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 45:84 )	A	45 - 84
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 85:105 )	A	85 - 105
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 106:119 )	A	106 - 119
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 120:133 )	A	120 - 133
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 134:174 )	A	134 - 174
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 175:195 )	A	175 - 195
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 1:10 )	B	1 - 10
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 11:48 )	B	11 - 48
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 49:65 )	B	49 - 65
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 66:93 )	B	66 - 93
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 94:119 )	B	94 - 119
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 120:149 )	B	120 - 149
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 150:166 )	B	150 - 166
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 167:194 )	B	167 - 194
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 201:201 )	B	201

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi