PDB-8s4s: PrgE from plasmid pCF10

ID or keywords:

Entry

Database: PDB / ID: 8s4s

Title

PrgE from plasmid pCF10

Components

PrgE

Keywords

DNA BINDING PROTEIN / SSB

Function / homology

: / PrgE

Function and homology information

Biological species

Enterococcus faecalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Breidenstein, A. / Berntsson, R.P.-A.

Funding support

Sweden, 3items

Citation

Journal: Life Sci Alliance / Year: 2024
Title: PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs.
Authors: Breidenstein, A. / Lamy, A. / Bader, C.P. / Sun, W.S. / Wanrooij, P.H. / Berntsson, R.P.

History

Deposition	Feb 22, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 29, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2024	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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8s4s.cif.gz	152.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8s4s_validation.pdf.gz	446.7 KB	Display	wwPDB validaton report
Full document	8s4s_full_validation.pdf.gz	447 KB	Display
Data in XML	8s4s_validation.xml.gz	11.2 KB	Display
Data in CIF	8s4s_validation.cif.gz	14.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s4/8s4s ftp://data.pdbj.org/pub/pdb/validation_reports/s4/8s4s	HTTPS FTP

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Related structure data

Related structure data	8s4tC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PrgE

B: PrgE

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, Gel filtration indicates a fluid oligomerisation varying from dimer to tetramer in vitro

Unit cell

Length a, b, c (Å)	58.175, 58.170, 87.099
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	PrgE / PrgK Mass: 17067.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) Gene: prgK, prgE, EGX33_13060, EU507_13905, F6H88_002583, FDO46_002730, H9Q64_07920, HRF81_13830, IHC34_002761, KCT30_002803, NAG05_14735 Production host: Escherichia coli (E. coli) / References: UniProt: D1LHE9
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.17 Å³/Da / Density % sol: 43.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M LiSO4, 0.1 M K Phos Cit pH 4.2, 20 %w/v PEG 1K

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 13, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 2.515→48.38 Å / Num. obs: 10486 / % possible obs: 99.6 % / Redundancy: 33.1 % / CC_1/2: 0.999 / R_rim(I) all: 0.139 / Net I/σ(I): 21.4
Reflection shell	Resolution: 2.515→2.56 Å / Redundancy: 35.04 % / Mean I/σ(I) obs: 2.39 / Num. unique obs: 537 / CC_1/2: 0.852 / R_rim(I) all: 1.718 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
XDS		data scaling
PHENIX	1.20.1-4487	phasing
Coot	0.9.6	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→48.377 Å / Cor.coef. F_o:F_c: 0.924 / Cor.coef. F_o:F_c free: 0.907 / WR_factor R_free: 0.268 / WR_factor R_work: 0.224 / SU B: 30.531 / SU ML: 0.289 / Average fsc free: 0.9423 / Average fsc work: 0.9604 / Cross valid method: THROUGHOUT / ESU R Free: 0.413
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2777	846	9.935 %	RANDOM
R_work	0.2345	7669	-	-
all	0.239	-	-	-
obs	-	8515	99.579 %	-

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: 61.93 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.315 Å²	0 Å²	0 Å²
2-	-	1.629 Å²	0 Å²
3-	-	-	2.686 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→48.377 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2126	0	11	19	2156

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	2181
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	1972
X-RAY DIFFRACTION	r_angle_refined_deg	0.67	1.652	2924
X-RAY DIFFRACTION	r_angle_other_deg	0.259	1.572	4620
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.51	5	257
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.2	5	10
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.401	10	416
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.708	10	121
X-RAY DIFFRACTION	r_chiral_restr	0.032	0.2	307
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	2455
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	437
X-RAY DIFFRACTION	r_nbd_refined	0.176	0.2	346
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.168	0.2	1664
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1009
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	1189
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	46
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.162	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.141	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.156	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	2.042	5.097	1034
X-RAY DIFFRACTION	r_mcbond_other	2.04	5.097	1034
X-RAY DIFFRACTION	r_mcangle_it	3.651	7.627	1289
X-RAY DIFFRACTION	r_mcangle_other	3.65	7.628	1290
X-RAY DIFFRACTION	r_scbond_it	1.563	5.331	1147
X-RAY DIFFRACTION	r_scbond_other	1.535	5.298	1140
X-RAY DIFFRACTION	r_scangle_it	2.824	7.897	1635
X-RAY DIFFRACTION	r_scangle_other	2.791	7.843	1624
X-RAY DIFFRACTION	r_lrange_it	6.284	75.879	2285
X-RAY DIFFRACTION	r_lrange_other	6.002	75.833	2283

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
2.7-2.77	0.419	52	0.327	564	0.335	616	0.926	0.945	100	0.278
2.77-2.846	0.335	43	0.303	543	0.305	586	0.933	0.947	100	0.254
2.846-2.928	0.359	83	0.301	509	0.309	593	0.905	0.943	99.8314	0.264
2.928-3.018	0.314	55	0.261	517	0.266	572	0.941	0.957	100	0.229
3.018-3.116	0.433	55	0.28	492	0.293	547	0.896	0.953	100	0.249
3.116-3.225	0.345	53	0.256	491	0.263	544	0.924	0.958	100	0.232
3.225-3.346	0.354	45	0.284	464	0.289	509	0.928	0.948	100	0.251
3.346-3.482	0.289	59	0.251	441	0.255	500	0.955	0.962	100	0.234
3.482-3.636	0.267	53	0.241	453	0.243	507	0.956	0.966	99.8028	0.232
3.636-3.812	0.297	41	0.249	397	0.254	443	0.948	0.964	98.8713	0.244
3.812-4.017	0.255	40	0.228	363	0.231	429	0.963	0.969	93.9394	0.219
4.017-4.259	0.325	31	0.191	388	0.2	419	0.934	0.974	100	0.187
4.259-4.551	0.217	42	0.192	368	0.195	411	0.97	0.977	99.7567	0.186
4.551-4.912	0.207	51	0.188	312	0.191	363	0.973	0.979	100	0.191
4.912-5.375	0.232	19	0.205	324	0.207	343	0.97	0.976	100	0.206
5.375-6	0.252	44	0.208	268	0.215	312	0.973	0.975	100	0.214
6-6.911	0.264	23	0.219	261	0.223	284	0.969	0.971	100	0.221
6.911-8.421	0.247	22	0.2	225	0.204	247	0.969	0.973	100	0.217
8.421-11.733	0.213	19	0.184	180	0.186	199	0.979	0.98	100	0.212
11.733-48.377	0.309	14	0.375	110	0.368	126	0.936	0.907	98.4127	0.431

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	0.4995	0.1448	0.6358	0.2355	-0.2691	1.8889	0.0867	0.0855	0.003	-0.0142	-0.0188	0.0238	0.2286	0.173	-0.0678	0.1391	0.0667	-0.0184	0.1165	0.01	0.0964	-13.7594	-12.6941	6.7289
2	0.5655	0.4042	-0.348	0.2902	-0.2261	1.1821	-0.0428	-0.0111	0.1967	-0.0429	-0.0112	0.1509	-0.1293	0.0057	0.054	0.1883	0.0408	-0.0944	0.0108	-0.0103	0.1842	-14.1799	12.6553	7.9431

Refinement TLS group

Selection: ALL

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