PDB-5com: Crystal structure of Uncharacterized Protein Q187F5 from Clostrid...

ID or keywords:

Entry

Database: PDB / ID: 5com

Title

Crystal structure of Uncharacterized Protein Q187F5 from Clostridium difficile 630

Components

Putative conjugative transposon protein Tn1549-like, CTn5-Orf2

Keywords

UNKNOWN FUNCTION / DUF1706 / DfsB / replication

Function / homology

Protein of unknown function DUF1706 / Protein of unknown function (DUF1706) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / D(-)-TARTARIC ACID / Conjugative transposon protein Tn1549-like, CTn5-Orf2

Function and homology information

Biological species

Peptoclostridium difficile 630 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Taylor, J.D. / Taylor, G. / Matthews, S.J.

Citation

Journal: J.Mol.Biol. / Year: 2016
Title: Structures of the DfsB Protein Family Suggest a Cationic, Helical Sibling Lethal Factor Peptide.
Authors: Taylor, J.D. / Taylor, G. / Hare, S.A. / Matthews, S.J.

History

Deposition	Jul 20, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2016	Group: Database references
Revision 1.2	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5com.cif.gz	170.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5com.ent.gz	135.7 KB	Display	PDB format
PDBx/mmJSON format	5com.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5com_validation.pdf.gz	439.9 KB	Display	wwPDB validaton report
Full document	5com_full_validation.pdf.gz	442 KB	Display
Data in XML	5com_validation.xml.gz	20.2 KB	Display
Data in CIF	5com_validation.cif.gz	30.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/co/5com ftp://data.pdbj.org/pub/pdb/validation_reports/co/5com	HTTPS FTP

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Related structure data

Related structure data	5civC 5cofC 5cogC 5cqvC C: citing same article (ref.)
Similar structure data	2dvp-d 2a90-d 6ebu-d 4noh-2 4ygu-4 2zti-d 4a1k-d 4ai4-d 5civ-d 6n90-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
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (1)

Deposited unit

A: Putative conjugative transposon protein Tn1549-like, CTn5-Orf2

B: Putative conjugative transposon protein Tn1549-like, CTn5-Orf2

hetero molecules

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

1

A: Putative conjugative transposon protein Tn1549-like, CTn5-Orf2

hetero molecules

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

2

B: Putative conjugative transposon protein Tn1549-like, CTn5-Orf2

hetero molecules

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

Unit cell

Length a, b, c (Å)	127.050, 50.300, 91.720
Angle α, β, γ (deg.)	90.00, 118.70, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Putative conjugative transposon protein Tn1549-like, CTn5-Orf2 Mass: 22141.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptoclostridium difficile 630 (bacteria) Gene: CD630_18460 / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q187F5
#2: Chemical	ChemComp-TAR / D(-)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.11 Å³/Da / Density % sol: 60.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Sodium formate, 0.1 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate, 0.1 M Sodium potassium tartrate tetrahydrate, 0.1 M Sodium oxamate 0.1 M Tris, 0.1 M Bicine, pH 8.5, ...Details: 0.1 M Sodium formate, 0.1 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate, 0.1 M Sodium potassium tartrate tetrahydrate, 0.1 M Sodium oxamate 0.1 M Tris, 0.1 M Bicine, pH 8.5, 12% PEG 550 MME, 6% PEG 20,000

Crystal

Density Matthews: 3.11 Å³/Da / Density % sol: 60.4 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Sodium formate, 0.1 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate, 0.1 M Sodium potassium tartrate tetrahydrate, 0.1 M Sodium oxamate 0.1 M Tris, 0.1 M Bicine, pH 8.5, ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 28, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.85→61.74 Å / Num. obs: 80903 / % possible obs: 95.4 % / Redundancy: 7 % / R_merge(I) obs: 0.073 / Net I/σ(I): 15.8
Reflection shell	Resolution: 1.85→1.9 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.63 / Mean I/σ(I) obs: 2.4 / % possible all: 69.4

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PHENIX	1.9_1692	phasing
xia2		data reduction
xia2		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.85→61.74 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.85 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.1943	3891	4.81 %
R_work	0.1706	-	-
obs	0.1718	80903	95.12 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.85→61.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2914	0	11	499	3424

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3035
X-RAY DIFFRACTION	f_angle_d	1.078	4117
X-RAY DIFFRACTION	f_dihedral_angle_d	12.91	1151
X-RAY DIFFRACTION	f_chiral_restr	0.051	439
X-RAY DIFFRACTION	f_plane_restr	0.005	521

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8501-1.8727	0.3052	100	0.2684	1985	X-RAY DIFFRACTION	68
1.8727-1.8964	0.2693	102	0.2559	2025	X-RAY DIFFRACTION	69
1.8964-1.9214	0.2603	114	0.252	2220	X-RAY DIFFRACTION	77
1.9214-1.9477	0.345	110	0.2434	2245	X-RAY DIFFRACTION	78
1.9477-1.9755	0.2596	127	0.2277	2508	X-RAY DIFFRACTION	87
1.9755-2.005	0.2674	138	0.2123	2742	X-RAY DIFFRACTION	93
2.005-2.0363	0.2206	140	0.2024	2761	X-RAY DIFFRACTION	98
2.0363-2.0697	0.2186	145	0.1897	2917	X-RAY DIFFRACTION	100
2.0697-2.1054	0.2609	147	0.1876	2859	X-RAY DIFFRACTION	99
2.1054-2.1437	0.1557	142	0.1791	2868	X-RAY DIFFRACTION	100
2.1437-2.1849	0.198	148	0.1667	2909	X-RAY DIFFRACTION	100
2.1849-2.2295	0.1729	139	0.1676	2846	X-RAY DIFFRACTION	100
2.2295-2.278	0.217	150	0.1695	2948	X-RAY DIFFRACTION	100
2.278-2.331	0.1897	141	0.1623	2818	X-RAY DIFFRACTION	100
2.331-2.3893	0.2042	145	0.1646	2908	X-RAY DIFFRACTION	100
2.3893-2.4539	0.1938	146	0.1643	2839	X-RAY DIFFRACTION	100
2.4539-2.5261	0.1852	150	0.1664	2953	X-RAY DIFFRACTION	100
2.5261-2.6077	0.2015	141	0.1682	2850	X-RAY DIFFRACTION	100
2.6077-2.7009	0.198	144	0.1593	2884	X-RAY DIFFRACTION	100
2.7009-2.809	0.1891	146	0.1625	2876	X-RAY DIFFRACTION	100
2.809-2.9368	0.1874	147	0.1615	2891	X-RAY DIFFRACTION	100
2.9368-3.0917	0.1885	145	0.1729	2876	X-RAY DIFFRACTION	100
3.0917-3.2854	0.153	145	0.1695	2890	X-RAY DIFFRACTION	100
3.2854-3.539	0.1889	150	0.1632	2851	X-RAY DIFFRACTION	100
3.539-3.8951	0.164	146	0.1511	2907	X-RAY DIFFRACTION	100
3.8951-4.4586	0.1728	150	0.1412	2866	X-RAY DIFFRACTION	100
4.4586-5.6168	0.1849	146	0.1571	2891	X-RAY DIFFRACTION	100
5.6168-61.7755	0.2075	147	0.1915	2879	X-RAY DIFFRACTION	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	0.4858	-0.3919	-0.1447	2.1317	-0.0736	0.244	-0.1554	-0.2822	0.1467	0.6366	0.1606	-0.11	-0.0711	0.0568	0.0003	0.1615	0.0032	-0.0246	0.1901	-0.0393	0.2094	27.731	8.6772	46.9244
2	0.1072	-0.0799	0.1678	0.2042	-0.1222	0.2363	0.076	0.0324	0.0461	-0.0028	-0.0612	-0.0274	0.2151	0.1275	0	0.1517	0.0015	-0.0119	0.145	0.007	0.208	28.5401	-15.4367	45.7729
3	0.0996	0.0811	0.0787	0.2275	0.0295	0.0771	0.0244	0.0273	-0.0363	-0.2839	0.0459	-0.0481	0.0818	0.0595	0.0079	0.1278	-0.0124	0.0141	0.1289	-0.0122	0.1342	21.8548	1.2083	33.6196
4	0.2327	0.0175	0.0443	0.0049	-0.0063	0.03	-0.2457	0.6651	0.3448	-0.4517	0.049	-0.0392	-0.084	0.1144	0.0001	0.3751	-0.0253	-0.0481	0.2769	0.0446	0.3156	13.4972	4.556	24.5443
5	0.0478	-0.0599	0.0367	0.1021	-0.135	0.4817	-0.0066	0.1285	-0.151	-0.0482	-0.0027	0.039	0.085	-0.0099	0.0003	0.1451	-0.0231	-0.002	0.1418	-0.0209	0.1706	17.2233	-8.1259	32.7238
6	0.4616	-0.2392	0.1742	1.4853	-0.3157	0.428	0.1123	0.1531	0.1435	-0.2302	-0.1202	-0.1259	0.038	0.0122	0.0031	0.1288	-0.0494	0.031	0.1738	-0.0387	0.1986	30.9614	3.8814	35.8112
7	2.1256	1.4819	0.8305	1.7363	1.2868	1.0246	-0.2875	0.0226	0.3001	-0.4959	0.0602	0.4279	-0.2329	-0.0307	-0.134	0.1759	0.0057	-0.0013	0.1518	-0.007	0.2895	12.1798	14.4802	35.5667
8	0.3333	0.099	-0.2579	0.6483	-0.2129	0.2347	-0.1023	-0.1904	-0.0794	0.3375	0.1599	0.2148	-0.0364	-0.1412	-0.0049	0.1499	0.0022	-0.0145	0.1739	-0.011	0.1325	23.7576	-2.23	48.0922
9	0.24	0.0007	0.1659	0.5115	-0.0927	0.344	-0.008	0.0374	-0.0448	-0.0176	0.1416	-0.3737	0.2791	0.4583	0.0132	0.2501	0.0318	-0.0042	0.2123	-0.0124	0.1507	40.0631	14.777	17.3998
10	0.4173	-0.0286	0.1018	0.4062	0.2396	0.1803	-0.0372	0.1426	0.2821	-0.1699	0.1165	-0.0882	-0.0722	0.0257	-0.0153	0.1768	-0.0403	-0.0131	0.1889	0.0234	0.1803	38.4245	38.5514	20.0017
11	0.4613	-0.0719	-0.6426	0.8929	0.1118	1.0669	-0.0078	0.0421	0.1814	-0.1575	-0.0912	0.198	0.0024	-0.2969	-0.0157	0.1308	-0.0018	-0.018	0.2073	0.0161	0.1314	24.0643	25.7042	10.3727
12	1.3277	0.7715	0.0155	1.596	-0.0531	0.6138	-0.0456	0.0597	0.0073	-0.1968	-0.0574	0.3331	0.2393	-0.1029	-0.2624	0.2339	-0.0197	0.0069	0.1714	0.025	0.1216	29.1267	18.4084	21.5399
13	0.3619	-0.2423	-0.0372	0.2128	0.1169	0.1132	0.0844	0.2298	-0.0982	-0.2983	0.0088	0.2645	0.2587	-0.2364	0.001	0.3527	-0.0376	-0.017	0.2734	-0.0318	0.1989	27.4363	9.3582	2.1614
14	0.2393	0.1884	-0.1006	0.1792	-0.0674	0.4699	0.0468	0.1688	-0.0479	-0.0255	0.1211	-0.2964	0.1443	0.2722	0.0147	0.138	-0.0221	0.011	0.2086	-0.0105	0.158	40.6136	25.6529	13.9975

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 54 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 55 through 77 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 78 through 87 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 88 through 109 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 110 through 130 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 131 through 155 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 156 through 183 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 13 through 36 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 37 through 54 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 55 through 109 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 110 through 130 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 131 through 155 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 156 through 183 )

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