PDB-5znm: Colicin D Central Domain and C-terminal tRNase domain

ID or keywords:

Entry

Database: PDB / ID: 5znm

Title

Colicin D Central Domain and C-terminal tRNase domain

Components

Colicin-D

Keywords

ANTIBIOTIC /

Colicin /

bacteriocin / tRNAse / membrane translocation.

Function / homology

Function and homology information

extrachromosomal circular DNA / RNA nuclease activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Chang, J.W. / Sato, Y. / Ogawa, T. / Arakawa, T. / Fukai, S. / Fushinobu, S. / Masaki, H.

Funding support

Japan, 1items

Citation

Journal: J. Biochem. / Year: 2018
Title: Crystal structure of the central and the C-terminal RNase domains of colicin D implicated its translocation pathway through inner membrane of target cell
Authors: Chang, J.W. / Sato, Y. / Ogawa, T. / Arakawa, T. / Fukai, S. / Fushinobu, S. / Masaki, H.

History

Deposition	Apr 10, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 29, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 31, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Mar 27, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5znm.cif.gz	287.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5znm.ent.gz	232.8 KB	Display	PDB format
PDBx/mmJSON format	5znm.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/zn/5znm ftp://data.pdbj.org/pub/pdb/validation_reports/zn/5znm	HTTPS FTP

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Related structure data

Similar structure data	1pwv-1 30249 0993 30682 2w45-d 30003 2w4b-d 30345 20277 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

Deposited unit

A: Colicin-D

B: Colicin-D

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, Monomer in solution., light scattering, Monomer in solution.

Unit cell

Length a, b, c (Å)	116.352, 146.115, 45.763
Angle α, β, γ (deg.)	90.00, 102.49, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-942- HOH
2	1	A-962- HOH
3	1	B-868- HOH

#1: Protein	Colicin-D / CD-CRD Mass: 41609.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 W1485 / Gene: cda, colD / Production host: Escherichia coli (E. coli) / Strain (production host): W3110 / References: UniProt: P17998
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.28 Å³/Da / Density % sol: 46.1 % / Description: pillar
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES sodium pH 7.5, 2.5% v/v Polyethylene glycol 400, 2.2 M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2015 / Details: horizontal two step focusing
Radiation	Monochromator: liquid nitrogen-cooled Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. obs: 63995 / % possible obs: 96.4 % / Redundancy: 5.1 % / R_sym value: 0.08 / Net I/σ(I): 14.1
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.8 / R_sym value: 0.441 / % possible all: 93.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.85→44.842 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2123	3072	5.03 %
R_work	0.1716	-	-
obs	0.1737	61089	96.31 %

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→44.842 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5404	0	102	299	5805

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5578
X-RAY DIFFRACTION	f_angle_d	0.973	7549
X-RAY DIFFRACTION	f_dihedral_angle_d	14.134	3377
X-RAY DIFFRACTION	f_chiral_restr	0.062	863
X-RAY DIFFRACTION	f_plane_restr	0.005	980

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 (%)
1.8498-1.8787	0.3091	121	0.2587	2481	X-RAY DIFFRACTION	92
1.8787-1.9095	0.2921	143	0.2459	2470	X-RAY DIFFRACTION	90
1.9095-1.9425	0.2618	146	0.2235	2505	X-RAY DIFFRACTION	93
1.9425-1.9778	0.2672	129	0.204	2627	X-RAY DIFFRACTION	96
1.9778-2.0158	0.265	140	0.1926	2608	X-RAY DIFFRACTION	96
2.0158-2.057	0.2309	126	0.1858	2631	X-RAY DIFFRACTION	96
2.057-2.1017	0.235	151	0.1831	2640	X-RAY DIFFRACTION	96
2.1017-2.1506	0.2291	145	0.1744	2596	X-RAY DIFFRACTION	96
2.1506-2.2044	0.2242	136	0.1825	2681	X-RAY DIFFRACTION	98
2.2044-2.264	0.1878	127	0.1741	2673	X-RAY DIFFRACTION	97
2.264-2.3306	0.1961	155	0.1654	2649	X-RAY DIFFRACTION	97
2.3306-2.4058	0.2375	141	0.177	2623	X-RAY DIFFRACTION	96
2.4058-2.4918	0.2361	132	0.1756	2526	X-RAY DIFFRACTION	93
2.4918-2.5916	0.2461	145	0.1713	2706	X-RAY DIFFRACTION	98
2.5916-2.7095	0.2058	153	0.1651	2690	X-RAY DIFFRACTION	98
2.7095-2.8523	0.2276	121	0.1699	2710	X-RAY DIFFRACTION	98
2.8523-3.031	0.2085	133	0.177	2711	X-RAY DIFFRACTION	98
3.031-3.2649	0.2165	145	0.1708	2705	X-RAY DIFFRACTION	99
3.2649-3.5934	0.1924	116	0.1582	2615	X-RAY DIFFRACTION	95
3.5934-4.113	0.1727	165	0.15	2725	X-RAY DIFFRACTION	100
4.113-5.1808	0.1904	152	0.1426	2736	X-RAY DIFFRACTION	100
5.1808-44.855	0.2021	150	0.1829	2709	X-RAY DIFFRACTION	98

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	0.1282	-0.0314	-0.1289	0.0938	0.092	-0.0139	0.0633	-0.1855	0.0449	-0.0957	-0.0181	-0.2031	0.0409	0.0433	0.0001	0.1721	0.0083	0.0124	0.1776	0.0056	0.2132	53.9375	22.4543	10.3697
2	0.3167	0.0484	-0.1062	0.185	-0.3077	0.438	-0.0675	-0.0373	-0.0025	-0.0094	0.0192	0.0164	0.0126	-0.0148	-0	0.1821	-0.0346	-0.0047	0.1478	-0.0199	0.1896	35.2459	10.0236	-5.3688
3	0.1139	-0.1194	0.0348	0.4388	0.0133	0.047	0.2594	-0.0282	0.2241	-0.0985	0.1474	0.1628	-0.1926	-0.5189	0.0982	0.2545	0.014	0.1107	0.3106	0.0125	0.3619	17.1614	8.9149	11.8246
4	0.5837	0.3714	-0.0128	0.6149	-0.3667	0.2587	0.1059	-0.1133	0.1079	0.1876	-0.0744	0.2156	0.0055	-0.0756	0.0003	0.2052	-0.0277	0.0183	0.1931	-0.0142	0.1391	25.4156	5.2152	14.0458
5	-0.0197	0.2607	-0.3572	0.3367	-0.0783	0.371	-0.0207	0.056	-0.0772	-0.1299	0.0206	-0.0157	-0.0104	-0.0754	-0.0002	0.1484	-0.0182	-0.0058	0.1664	-0.0073	0.1918	35.0787	7.8502	-4.317
6	-0.0249	0.2778	0.4017	0.078	-0.0556	0.2786	0.0673	0.0041	0.0918	0.1484	-0.0282	0.0922	0.0333	-0.0546	0	0.1675	-0.0248	0.0215	0.1533	-0.0103	0.1748	26.7546	4.254	6.6477
7	0.7821	0.0017	0.2024	0.6538	0.3361	1.3453	0.0428	0.0266	0.0207	-0.0242	-0.0558	0.0477	-0.0232	-0.0534	-0.0004	0.1173	-0.0062	0.0076	0.1463	0.0056	0.1137	9.4387	-17.7991	-6.8912
8	0.2353	0.0409	-0.0816	0.1404	-0.0416	0.0567	0.1721	0.0754	-0.1824	0.0139	-0.1098	-0.0747	-0.066	0.0523	-0.0001	0.1671	-0.0035	-0.009	0.1949	0.0069	0.2118	53.7845	21.312	-10.4192
9	0.3087	0.0165	0.0434	0.5883	-0.2896	0.4371	-0.0465	-0.0446	-0.1084	0.0535	-0.0095	0.0458	-0.0315	-0.0454	0.0001	0.1525	0.0149	-0.0029	0.1424	-0.0083	0.1469	36.0335	34.805	6.0004
10	0.0802	-0.2058	-0.2013	0.9776	0.587	0.6683	-0.0557	0.0249	0.2366	0.1485	0.1165	0.7241	0.4341	-0.2401	-0.0942	0.1849	-0.0537	-0.1926	0.2802	0.1218	0.5706	17.8456	33.2528	-11.0418
11	0.4887	-0.0414	-0.0123	0.6331	-0.387	0.3436	0.0819	0.1647	-0.0677	-0.2177	-0.046	0.359	0.0102	-0.1392	-0.0006	0.2224	0.0076	-0.0592	0.2076	-0.0162	0.2048	25.3018	38.534	-14.1259
12	0.3347	-0.0574	0.1389	0.6814	-0.0098	0.1308	0.0067	-0.0646	-0.0681	0.0669	0.0142	0.1395	-0.0062	-0.0348	0	0.1447	0.0093	0.0108	0.1595	0.0078	0.1473	35.1305	35.9958	4.1251
13	0.0411	0.0756	0.1131	0.207	-0.0324	0.5522	-0.0482	-0.0546	-0.0797	-0.2124	0.0486	0.2736	-0.0637	-0.148	-0	0.199	0.0218	-0.0443	0.1798	-0.0041	0.2342	28.8969	35.8859	-8.6558
14	0.0556	-0.0845	-0.0705	0.0645	-0.1196	0.082	-0.0405	0.0889	-0.2021	-0.117	-0.0195	0.3021	-0.0255	-0.0235	0.0002	0.1733	0.0173	-0.0145	0.1357	-0.0203	0.1897	24.4774	43.6751	-4.0411
15	1.0463	0.0408	-0.3174	0.6403	0.7106	0.9712	0.1083	-0.0426	-0.0103	0.1165	-0.0655	0.0622	0.0496	-0.0138	-0.0001	0.1582	-0.0102	0.0105	0.1508	0.0116	0.2154	9.4632	61.6064	6.9262

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 311 through 332 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 333 through 384 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 385 through 435 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 436 through 491 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 492 through 552 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 553 through 601 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 602 through 697 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 311 through 332 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 333 through 380 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 381 through 435 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 436 through 491 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 492 through 552 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 553 through 583 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 584 through 601 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 602 through 697 )

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