PDB-6sif: Epidermicin antimicrobial protein from Staphylococcus epidermidis

ID or keywords:

Entry

Database: PDB / ID: 6sif

Title

Epidermicin antimicrobial protein from Staphylococcus epidermidis

Components

Epidermicin locus structural protein

Keywords

STRUCTURAL PROTEIN / antibiotic / helical

Function / homology

Bacteriocin class II, aureocin-like / Aureocin-like type II bacteriocin / Epidermicin locus structural protein

Function and homology information

Biological species

Staphylococcus epidermidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 1.69 Å

Authors

Derrick, J.P.

Funding support

United Kingdom, 1items

Citation

Journal: Iscience / Year: 2020
Title: Flowering Poration-A Synergistic Multi-Mode Antibacterial Mechanism by a Bacteriocin Fold.
Authors: Hammond, K. / Lewis, H. / Halliwell, S. / Desriac, F. / Nardone, B. / Ravi, J. / Hoogenboom, B.W. / Upton, M. / Derrick, J.P. / Ryadnov, M.G.

History

Deposition	Aug 9, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 26, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 24, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Mar 31, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	May 15, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6sif.cif.gz	177 KB	Display	PDBx/mmCIF format
PDB format	pdb6sif.ent.gz	143.5 KB	Display	PDB format
PDBx/mmJSON format	6sif.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6sif_validation.pdf.gz	488.3 KB	Display	wwPDB validaton report
Full document	6sif_full_validation.pdf.gz	493.3 KB	Display
Data in XML	6sif_validation.xml.gz	16 KB	Display
Data in CIF	6sif_validation.cif.gz	22.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/si/6sif ftp://data.pdbj.org/pub/pdb/validation_reports/si/6sif	HTTPS FTP

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Related structure data

Related structure data	6sigC C: citing same article (ref.)
Similar structure data	4a61-1 1pju-5 4m2z-d 2c5r-d 2f08-d 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: Epidermicin locus structural protein

B: Epidermicin locus structural protein

C: Epidermicin locus structural protein

D: Epidermicin locus structural protein

E: Epidermicin locus structural protein

F: Epidermicin locus structural protein

G: Epidermicin locus structural protein

H: Epidermicin locus structural protein

hetero molecules

49.2 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	92.180, 117.860, 52.930
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	ALA	ALA	A	A	1 - 51	1 - 51
2	1	MET	MET	ALA	ALA	B	B	1 - 51	1 - 51
1	2	MET	MET	ALA	ALA	A	A	1 - 51	1 - 51
2	2	MET	MET	ALA	ALA	C	C	1 - 51	1 - 51
1	3	MET	MET	LEU	LEU	A	A	1 - 49	1 - 49
2	3	MET	MET	LEU	LEU	D	D	1 - 49	1 - 49
1	4	ALA	ALA	TRP	TRP	A	A	2 - 50	2 - 50
2	4	ALA	ALA	TRP	TRP	E	E	2 - 50	2 - 50
1	5	MET	MET	ALA	ALA	A	A	1 - 51	1 - 51
2	5	MET	MET	ALA	ALA	F	F	1 - 51	1 - 51
1	6	ALA	ALA	LYS	LYS	A	A	2 - 47	2 - 47
2	6	ALA	ALA	LYS	LYS	G	G	2 - 47	2 - 47
1	7	ALA	ALA	TRP	TRP	A	A	2 - 50	2 - 50
2	7	ALA	ALA	TRP	TRP	H	H	2 - 50	2 - 50
1	8	MET	MET	ALA	ALA	B	B	1 - 51	1 - 51
2	8	MET	MET	ALA	ALA	C	C	1 - 51	1 - 51
1	9	MET	MET	LEU	LEU	B	B	1 - 49	1 - 49
2	9	MET	MET	LEU	LEU	D	D	1 - 49	1 - 49
1	10	ALA	ALA	TRP	TRP	B	B	2 - 50	2 - 50
2	10	ALA	ALA	TRP	TRP	E	E	2 - 50	2 - 50
1	11	MET	MET	ALA	ALA	B	B	1 - 51	1 - 51
2	11	MET	MET	ALA	ALA	F	F	1 - 51	1 - 51
1	12	ALA	ALA	LYS	LYS	B	B	2 - 47	2 - 47
2	12	ALA	ALA	LYS	LYS	G	G	2 - 47	2 - 47
1	13	ALA	ALA	TRP	TRP	B	B	2 - 50	2 - 50
2	13	ALA	ALA	TRP	TRP	H	H	2 - 50	2 - 50
1	14	MET	MET	LEU	LEU	C	C	1 - 49	1 - 49
2	14	MET	MET	LEU	LEU	D	D	1 - 49	1 - 49
1	15	ALA	ALA	TRP	TRP	C	C	2 - 50	2 - 50
2	15	ALA	ALA	TRP	TRP	E	E	2 - 50	2 - 50
1	16	MET	MET	ALA	ALA	C	C	1 - 51	1 - 51
2	16	MET	MET	ALA	ALA	F	F	1 - 51	1 - 51
1	17	ALA	ALA	LYS	LYS	C	C	2 - 47	2 - 47
2	17	ALA	ALA	LYS	LYS	G	G	2 - 47	2 - 47
1	18	ALA	ALA	TRP	TRP	C	C	2 - 50	2 - 50
2	18	ALA	ALA	TRP	TRP	H	H	2 - 50	2 - 50
1	19	ALA	ALA	LEU	LEU	D	D	2 - 49	2 - 49
2	19	ALA	ALA	LEU	LEU	E	E	2 - 49	2 - 49
1	20	MET	MET	LEU	LEU	D	D	1 - 49	1 - 49
2	20	MET	MET	LEU	LEU	F	F	1 - 49	1 - 49
1	21	ALA	ALA	LYS	LYS	D	D	2 - 47	2 - 47
2	21	ALA	ALA	LYS	LYS	G	G	2 - 47	2 - 47
1	22	ALA	ALA	LEU	LEU	D	D	2 - 49	2 - 49
2	22	ALA	ALA	LEU	LEU	H	H	2 - 49	2 - 49
1	23	ALA	ALA	TRP	TRP	E	E	2 - 50	2 - 50
2	23	ALA	ALA	TRP	TRP	F	F	2 - 50	2 - 50
1	24	ALA	ALA	LYS	LYS	E	E	2 - 47	2 - 47
2	24	ALA	ALA	LYS	LYS	G	G	2 - 47	2 - 47
1	25	ALA	ALA	ALA	ALA	E	E	2 - 51	2 - 51
2	25	ALA	ALA	ALA	ALA	H	H	2 - 51	2 - 51
1	26	ALA	ALA	LYS	LYS	F	F	2 - 47	2 - 47
2	26	ALA	ALA	LYS	LYS	G	G	2 - 47	2 - 47
1	27	ALA	ALA	TRP	TRP	F	F	2 - 50	2 - 50
2	27	ALA	ALA	TRP	TRP	H	H	2 - 50	2 - 50
1	28	ALA	ALA	LYS	LYS	G	G	2 - 47	2 - 47
2	28	ALA	ALA	LYS	LYS	H	H	2 - 47	2 - 47

NCS ensembles :

#1: Protein	Epidermicin locus structural protein Mass: 6054.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Staphylococcus epidermidis (bacteria) / References: UniProt: H9BG66
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.97 Å³/Da / Density % sol: 58.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium Sulphate, 0.1M Sodium Acetate pH4.5, 28% PEG 2000 MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0725 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0725 Å / Relative weight: 1
Reflection	Resolution: 1.69→46.13 Å / Num. obs: 64599 / % possible obs: 99 % / Redundancy: 4.4 % / B_iso Wilson estimate: 16.461 Å² / R_merge(I) obs: 0.058 / R_pim(I) all: 0.035 / R_rim(I) all: 0.075 / Net I/σ(I): 14.1
Reflection shell	Resolution: 1.69→1.73 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.576 / Num. unique obs: 4639 / R_pim(I) all: 0.351 / R_rim(I) all: 0.744 / % possible all: 97.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
PDB_EXTRACT	3.25	data extraction
xia2		data reduction
xia2		data scaling
SHELXCD		phasing

Refinement

Method to determine structure:

MIR / Resolution: 1.69→46.13 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.913 / SU B: 5.558 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.108
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.262	3263	5.1 %	RANDOM
R_work	0.2475	-	-	-
obs	0.2482	61278	98.73 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 83.11 Å² / B_iso mean: 24.78 Å² / B_iso min: 9.85 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.13 Å²	0 Å²	-0 Å²
2-	-	-0.96 Å²	0 Å²
3-	-	-	-0.17 Å²

Refinement step

Cycle: final / Resolution: 1.69→46.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3374	0	40	103	3517
B_iso mean	-	-	38.96	26.42	-
Num. residues	-	-	-	-	401

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	3508
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	3446
X-RAY DIFFRACTION	r_angle_refined_deg	1.468	1.62	4710
X-RAY DIFFRACTION	r_angle_other_deg	1.439	1.588	7972
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.297	5	393
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.968	23.78	127
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.384	15	692
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	433
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3645
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	779

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	1679	0.1
1	2	B	1679	0.1
2	1	A	1674	0.09
2	2	C	1674	0.09
3	1	A	1565	0.08
3	2	D	1565	0.08
4	1	A	1657	0.09
4	2	E	1657	0.09
5	1	A	1680	0.09
5	2	F	1680	0.09
6	1	A	1472	0.11
6	2	G	1472	0.11
7	1	A	1645	0.08
7	2	H	1645	0.08
8	1	B	1695	0.09
8	2	C	1695	0.09
9	1	B	1587	0.08
9	2	D	1587	0.08
10	1	B	1644	0.1
10	2	E	1644	0.1
11	1	B	1703	0.09
11	2	F	1703	0.09
12	1	B	1461	0.12
12	2	G	1461	0.12
13	1	B	1628	0.09
13	2	H	1628	0.09
14	1	C	1589	0.07
14	2	D	1589	0.07
15	1	C	1646	0.09
15	2	E	1646	0.09
16	1	C	1692	0.09
16	2	F	1692	0.09
17	1	C	1467	0.11
17	2	G	1467	0.11
18	1	C	1611	0.09
18	2	H	1611	0.09
19	1	D	1544	0.11
19	2	E	1544	0.11
20	1	D	1557	0.11
20	2	F	1557	0.11
21	1	D	1444	0.12
21	2	G	1444	0.12
22	1	D	1534	0.08
22	2	H	1534	0.08
23	1	E	1678	0.07
23	2	F	1678	0.07
24	1	E	1500	0.09
24	2	G	1500	0.09
25	1	E	1674	0.1
25	2	H	1674	0.1
26	1	F	1488	0.09
26	2	G	1488	0.09
27	1	F	1628	0.1
27	2	H	1628	0.1
28	1	G	1480	0.11
28	2	H	1480	0.11

LS refinement shell

Resolution: 1.69→1.734 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.358	234	-
R_work	0.332	4402	-
all	-	4636	-
obs	-	-	97.35 %

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	5.0496	0.1119	-0.3166	2.0647	0.7934	4.3543	0.0078	-0.0995	0.0832	0.1464	-0.0204	0.1507	-0.093	-0.2241	0.0127	0.0161	0.0059	0.0061	0.2195	-0.0133	0.1865	83.752	31.051	32.831
2	3.9389	0.029	0.3564	1.7929	0.3633	6.3014	0.1117	-0.1872	0.1035	0.1888	0.0646	-0.1708	0.061	-0.0176	-0.1763	0.0232	-0.0035	-0.0125	0.1641	0.0052	0.1585	57.221	30.164	32.862
3	2.236	-0.14	-0.4549	4.9218	-1.3469	4.1261	-0.0142	0.2894	0.0449	-0.5076	-0.0088	-0.1075	0.227	0.0469	0.023	0.2178	0.0232	-0.0008	0.2176	0.0018	0.1999	69.861	8.996	33.785
4	2.0617	0.4659	-0.1318	4.747	-0.1839	3.0975	0.0404	-0.1638	-0.2182	0.4746	0.0184	-0.3553	0.1155	0.1308	-0.0588	0.1942	-0.026	-0.0051	0.1729	-0.0101	0.2384	72.534	48.6	9.433
5	4.9651	0.362	1.7979	1.6902	0.6985	4.2613	0.0118	0.3535	-0.1026	-0.2454	0.0257	0.0621	0.0843	0.0438	-0.0374	0.0446	-0.0046	-0.0048	0.2774	-0.0333	0.1938	83.717	25.424	11.036
6	3.3734	-0.4451	-1.3199	2.0797	0.1744	6.1889	0.0898	0.242	-0.0251	-0.3018	0.0799	-0.0143	-0.082	-0.2316	-0.1697	0.0445	-0.0054	0.0055	0.1582	0.0168	0.145	57.193	29.232	10.435
7	3.0849	0.5569	-0.1435	5.0331	1.9487	4.4818	-0.0093	0.4776	-0.3257	-0.2569	0.1839	-0.2962	-0.0272	0.2028	-0.1745	0.1591	-0.0388	0.042	0.2701	-0.0639	0.2794	73.487	48.598	40.742
8	1.5889	-0.3116	0.2321	5.1258	1.7509	2.6879	-0.0224	-0.2127	0.0618	0.1404	0.035	-0.0951	-0.0367	0.0912	-0.0126	0.147	0.0205	0.0399	0.1863	-0.0018	0.197	70.913	8.983	3.014

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 51
2	X-RAY DIFFRACTION	2	B	1 - 51
3	X-RAY DIFFRACTION	3	C	1 - 51
4	X-RAY DIFFRACTION	4	D	1 - 50
5	X-RAY DIFFRACTION	5	E	2 - 51
6	X-RAY DIFFRACTION	6	F	1 - 51
7	X-RAY DIFFRACTION	7	G	2 - 48
8	X-RAY DIFFRACTION	8	H	2 - 51

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