PDB-8qty: LytR LCP domain from Streptococcus dysgalactiae subs. dysgalactiae

ID or keywords:

Entry

Database: PDB / ID: 8qty

Title

LytR LCP domain from Streptococcus dysgalactiae subs. dysgalactiae

Components

Biofilm regulatory protein

Keywords

TRANSFERASE / LytR-CpsA-Psr / Wall teichoic acids

Function / homology

: / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Biofilm regulatory protein

Function and homology information

Biological species

Streptococcus dysgalactiae subsp. dysgalactiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Paquete-Ferreira, J. / Romao, M.J. / Santos-Silva, T.

Funding support

Portugal, 1items

Citation

Journal: Front Chem / Year: 2024
Title: Structural insights of an LCP protein-LytR-from Streptococcus dysgalactiae subs. dysgalactiae through biophysical and in silico methods.
Authors: Paquete-Ferreira, J. / Freire, F. / Fernandes, H.S. / Muthukumaran, J. / Ramos, J. / Bryton, J. / Panjkovich, A. / Svergun, D. / Santos, M.F.A. / Correia, M.A.S. / Fernandes, A.R. / Romao, M. ...

History

Deposition	Oct 13, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 4, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8qty.cif.gz	279.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8qty.ent.gz	177.3 KB	Display	PDB format
PDBx/mmJSON format	8qty.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8qty_validation.pdf.gz	450.8 KB	Display	wwPDB validaton report
Full document	8qty_full_validation.pdf.gz	458.9 KB	Display
Data in XML	8qty_validation.xml.gz	13.8 KB	Display
Data in CIF	8qty_validation.cif.gz	17.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qt/8qty ftp://data.pdbj.org/pub/pdb/validation_reports/qt/8qty	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	SASBDB: SASDTG2associated SAS data SASBDB: SASDTH2associated SAS data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Biofilm regulatory protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	141.271, 141.271, 133.742
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	97
Space group name H-M	I422

Components on special symmetry positions

ID	Model	Components
1	1	A-525- HOH

#1: Protein	Biofilm regulatory protein / LytR / BrpA Mass: 33664.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus dysgalactiae subsp. dysgalactiae (bacteria) Strain: VSD9 / Gene: lytR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A7LTX5
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 4.96 Å³/Da / Density % sol: 75.18 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 2.2 M ammonium sulphate 20% glycerol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.966 Å / Relative weight: 1
Reflection	Resolution: 2.8→48.608 Å / Num. obs: 16955 / % possible obs: 99.9 % / Redundancy: 8 % / CC_1/2: 0.999 / Net I/σ(I): 15.5
Reflection shell	Resolution: 2.8→2.95 Å / Num. unique obs: 2436 / CC_1/2: 0.666

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
Aimless		data scaling
MrBUMP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→48.608 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.907 / WR_factor R_free: 0.291 / WR_factor R_work: 0.263 / SU B: 37.551 / SU ML: 0.324 / Average fsc free: 0.9284 / Average fsc work: 0.9377 / Cross valid method: FREE R-VALUE / ESU R: 0.409 / ESU R Free: 0.303
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2927	895	5.279 %
R_work	0.2714	16060	-
all	0.272	-	-
obs	-	16955	99.776 %

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: 80.154 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.932 Å²	0 Å²	-0 Å²
2-	-	-0.932 Å²	0 Å²
3-	-	-	1.865 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→48.608 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2076	0	15	25	2116

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.012	2111
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2047
X-RAY DIFFRACTION	r_ext_dist_refined_b	0	0.01	7919
X-RAY DIFFRACTION	r_angle_refined_deg	1.968	1.654	2857
X-RAY DIFFRACTION	r_angle_other_deg	0.623	1.572	4712
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.143	5	268
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	18.605	5	11
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	24.182	10	388
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.352	10	91
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	341
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2453
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	445
X-RAY DIFFRACTION	r_nbd_refined	0.249	0.2	370
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.225	0.2	1921
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1042
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1285
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	44
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.722	0.2	63
X-RAY DIFFRACTION	r_nbd_other	0.517	0.2	81
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.691	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	4.044	5.429	1078
X-RAY DIFFRACTION	r_mcbond_other	4.044	5.429	1078
X-RAY DIFFRACTION	r_mcangle_it	5.689	9.809	1344
X-RAY DIFFRACTION	r_mcangle_other	5.687	9.809	1345
X-RAY DIFFRACTION	r_scbond_it	2.661	5.69	1033
X-RAY DIFFRACTION	r_scbond_other	2.678	5.686	1020
X-RAY DIFFRACTION	r_scangle_it	4.475	10.442	1513
X-RAY DIFFRACTION	r_scangle_other	4.5	10.434	1496
X-RAY DIFFRACTION	r_lrange_it	6.437	68.047	8808
X-RAY DIFFRACTION	r_lrange_other	6.437	68.044	8808

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
2.8-2.873	0.401	81	0.378	1140	0.38	1223	0.874	0.885	99.8365	0.361
2.873-2.951	0.354	74	0.355	1130	0.355	1205	0.896	0.904	99.917	0.339
2.951-3.036	0.37	53	0.352	1103	0.353	1157	0.914	0.912	99.9136	0.324
3.036-3.129	0.364	64	0.34	1071	0.341	1135	0.915	0.922	100	0.307
3.129-3.231	0.279	52	0.314	1059	0.312	1112	0.948	0.934	99.9101	0.277
3.231-3.344	0.287	75	0.324	989	0.321	1065	0.942	0.93	99.9061	0.294
3.344-3.47	0.356	62	0.305	959	0.308	1021	0.91	0.939	100	0.275
3.47-3.611	0.365	50	0.28	950	0.285	1000	0.923	0.952	100	0.257
3.611-3.77	0.281	38	0.297	917	0.296	956	0.936	0.939	99.8954	0.275
3.77-3.953	0.305	51	0.279	861	0.28	915	0.929	0.947	99.6721	0.265
3.953-4.166	0.214	30	0.246	857	0.245	888	0.972	0.961	99.8874	0.234
4.166-4.416	0.249	56	0.249	767	0.249	824	0.962	0.961	99.8786	0.241
4.416-4.718	0.25	41	0.221	730	0.223	773	0.961	0.969	99.7413	0.221
4.718-5.092	0.258	31	0.23	714	0.231	746	0.96	0.966	99.866	0.234
5.092-5.572	0.348	31	0.274	641	0.277	675	0.921	0.955	99.5556	0.278
5.572-6.22	0.387	29	0.306	587	0.31	618	0.943	0.945	99.6764	0.311
6.22-7.163	0.319	22	0.272	528	0.274	556	0.937	0.956	98.9209	0.276
7.163-8.725	0.307	21	0.236	453	0.239	477	0.927	0.966	99.3711	0.26
8.725-12.145	0.193	20	0.194	372	0.194	393	0.981	0.977	99.7455	0.216
12.145-48.608	0.265	14	0.344	232	0.339	247	0.975	0.934	99.5951	0.352

Refinement TLS params.

Method: refined / Origin x: -16.7071 Å / Origin y: -27.784 Å / Origin z: -18.4244 Å

	11	12	13	21	22	23	31	32	33
T	0.17 Å²	-0.0759 Å²	-0.0937 Å²	-	0.0798 Å²	0.0004 Å²	-	-	0.1695 Å²
L	5.0681 °²	-0.8968 °²	0.1769 °²	-	2.7598 °²	0.2493 °²	-	-	1.135 °²
S	-0.0727 Å °	0.035 Å °	-0.1776 Å °	0.0166 Å °	0.182 Å °	0.0527 Å °	0.2897 Å °	-0.0409 Å °	-0.1093 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	57 - 334
2	X-RAY DIFFRACTION	1		A	401 - 403

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi