PDB-7epj: Crystal structure of E.coli CcdB mutant V46L

ID or keywords:

Entry

Database: PDB / ID: 7epj

Title

Crystal structure of E.coli CcdB mutant V46L

Components

Toxin CcdB

Keywords

TOXIN / CcdB / Topoisomerase poison / global suppressor

Function / homology

Function and homology information

DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / toxin-antitoxin complex / negative regulation of DNA-templated DNA replication / plasmid maintenance / transcription repressor complex / negative regulation of DNA-templated transcription
Similarity search - Function

Biological species

Escherichia coli K-12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.354 Å

Authors

Manjunath, K. / Goyal, P. / Varadarajan, R.

Funding support

India, 2items

Citation

Journal: Plos Genet. / Year: 2022
Title: Mechanistic insights into global suppressors of protein folding defects.
Authors: Chattopadhyay, G. / Bhowmick, J. / Manjunath, K. / Ahmed, S. / Goyal, P. / Varadarajan, R.

History

Deposition	Apr 26, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 8, 2022	Provider: repository / Type: Initial release
Revision 1.1	Dec 21, 2022	Group: Database references / Derived calculations / Category: atom_type / citation / citation_author Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7epj.cif.gz	41.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7epj.ent.gz	24.8 KB	Display	PDB format
PDBx/mmJSON format	7epj.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/ep/7epj ftp://data.pdbj.org/pub/pdb/validation_reports/ep/7epj	HTTPS FTP

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Related structure data

Related structure data	7epgC 7epiC 3vubS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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: Toxin CcdB

hetero molecules

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

1

A: Toxin CcdB

hetero molecules

A: Toxin CcdB

hetero molecules

defined by author&software
Evidence: gel filtration
23.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.100, 36.760, 35.910
Angle α, β, γ (deg.)	90.000, 115.190, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-636- HOH
2	1	A-667- HOH

#1: Protein	Toxin CcdB / Cytotoxic protein CcdB / LynB / Protein G / Protein LetD Mass: 11735.535 Da / Num. of mol.: 1 / Mutation: V46L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ccdB, G, letB, letD, ECOK12F043 / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10Gyrase / References: UniProt: P62554
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.92 Å³/Da / Density % sol: 36 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 200mM CaCl2, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.0358 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0358 Å / Relative weight: 1
Reflection	Resolution: 1.35→33.98 Å / Num. obs: 19433 / % possible obs: 100 % / Redundancy: 5.9 % / B_iso Wilson estimate: 5.8 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.098 / R_pim(I) all: 0.043 / R_rim(I) all: 0.108 / Net I/σ(I): 11.6
Reflection shell	Resolution: 1.35→1.43 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.288 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2799 / CC_1/2: 0.928 / R_pim(I) all: 0.141 / R_rim(I) all: 0.322 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
MOSFLM	7.2.2	data reduction
SCALA	3.3.22	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3VUB

3vub

Resolution: 1.354→33.979 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.957 / WR_factor R_free: 0.185 / WR_factor R_work: 0.159 / SU B: 0.907 / SU ML: 0.038 / Average fsc free: 0.9456 / Average fsc work: 0.9501 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1844	855	4.401 %
R_work	0.1616	18574	-
all	0.163	-	-
obs	-	19429	99.979 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 9.358 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.031 Å²	-0 Å²	-0.123 Å²
2-	-	0.276 Å²	0 Å²
3-	-	-	-0.132 Å²

Refinement step

Cycle: LAST / Resolution: 1.354→33.979 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	792	0	2	167	961

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	834
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	781
X-RAY DIFFRACTION	r_angle_refined_deg	1.922	1.637	1133
X-RAY DIFFRACTION	r_angle_other_deg	1.515	1.575	1810
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.444	5	108
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.249	21.667	42
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.47	15	148
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.625	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	109
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	932
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	178
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	149
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	742
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	418
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.093	0.2	368
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.253	0.2	121
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.086	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.377	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.258	0.2	57
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.3	0.2	25
X-RAY DIFFRACTION	r_mcbond_it	1.227	0.862	411
X-RAY DIFFRACTION	r_mcbond_other	1.223	0.857	410
X-RAY DIFFRACTION	r_mcangle_it	1.884	1.29	514
X-RAY DIFFRACTION	r_mcangle_other	1.887	1.296	515
X-RAY DIFFRACTION	r_scbond_it	1.547	0.901	423
X-RAY DIFFRACTION	r_scbond_other	1.547	0.898	423
X-RAY DIFFRACTION	r_scangle_it	2.351	1.29	615
X-RAY DIFFRACTION	r_scangle_other	2.349	1.289	615
X-RAY DIFFRACTION	r_lrange_it	4.686	11.689	1014
X-RAY DIFFRACTION	r_lrange_other	4.385	10.371	956

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.354-1.389	0.213	70	0.172	1352	0.174	1422	0.937	0.946	100	0.157
1.389-1.427	0.196	73	0.174	1301	0.175	1374	0.928	0.935	100	0.159
1.427-1.468	0.21	67	0.195	1271	0.196	1338	0.924	0.936	100	0.182
1.468-1.514	0.173	62	0.174	1276	0.174	1338	0.956	0.951	100	0.159
1.514-1.563	0.186	48	0.169	1220	0.17	1268	0.951	0.954	100	0.153
1.563-1.618	0.194	55	0.162	1174	0.164	1230	0.947	0.953	99.9187	0.15
1.618-1.679	0.17	53	0.17	1136	0.17	1189	0.95	0.949	100	0.15
1.679-1.747	0.252	34	0.209	1136	0.21	1170	0.915	0.925	100	0.185
1.747-1.825	0.252	38	0.189	1037	0.191	1075	0.915	0.932	100	0.167
1.825-1.913	0.223	49	0.188	1001	0.19	1050	0.919	0.93	100	0.17
1.913-2.017	0.19	40	0.176	964	0.177	1006	0.951	0.948	99.8012	0.166
2.017-2.138	0.201	30	0.152	928	0.154	958	0.953	0.962	100	0.144
2.138-2.285	0.178	20	0.176	870	0.176	891	0.957	0.956	99.8878	0.167
2.285-2.468	0.145	17	0.127	820	0.127	837	0.969	0.976	100	0.129
2.468-2.702	0.114	34	0.126	741	0.125	775	0.977	0.977	100	0.129
2.702-3.018	0.179	37	0.147	660	0.149	697	0.967	0.968	100	0.159
3.018-3.48	0.191	33	0.149	578	0.152	611	0.964	0.969	100	0.166
3.48-4.252	0.155	55	0.14	481	0.142	536	0.971	0.973	100	0.159
4.252-5.966	0.191	25	0.139	396	0.142	421	0.972	0.974	100	0.167
5.966-33.979	0.233	15	0.182	231	0.184	246	0.944	0.958	100	0.219

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