PDB-7qd7: TarM(Se)_G117R

ID or keywords:

Entry

Database: PDB / ID: 7qd7

Title

TarM(Se)_G117R

Components

TarM(Se)_G117R

Keywords

TRANSFERASE /

Staphylococcus epidermidis /

glycosyltransferase / GT-B fold / alpha-O-glucose / wall teichoic acid

Function / homology

PHOSPHATE ION

Function and homology information

Biological species

Escherichia coli BL21 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 2.06 Å

Authors

Guo, Y. / Stehle, T.

Funding support

Germany, 1items

Citation

Journal: Sci Adv / Year: 2023
Title: Invasive Staphylococcus epidermidis uses a unique processive wall teichoic acid glycosyltransferase to evade immune recognition.
Authors: Guo, Y. / Du, X. / Krusche, J. / Beck, C. / Ali, S. / Walter, A. / Winstel, V. / Mayer, C. / Codee, J.D.C. / Peschel, A. / Stehle, T.

History

Deposition	Nov 26, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 10, 2023	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7qd7.cif.gz	122.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7qd7.ent.gz		Display	PDB format
PDBx/mmJSON format	7qd7.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/qd/7qd7 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/7qd7	HTTPS FTP

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Related structure data

Related structure data	7qh9C 7qntC 8p1xC 8p20C 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

AAA: TarM(Se)_G117R

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	58.680, 88.420, 97.490
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules AAA

#1: Protein	TarM(Se)_G117R Mass: 59652.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Production host: Staphylococcus epidermidis (bacteria)

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Non-polymers , 5 types, 225 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.12 Å³/Da / Density % sol: 41.98 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 10% PEG 20 000, 25% PEG MME 550, 0.1 M MES/imidazole, pH 6.9, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 7, 2020
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.06→43.704 Å / Num. obs: 32047 / % possible obs: 100 % / Redundancy: 12.8 % / CC_1/2: 0.99 / Net I/σ(I): 14.93
Reflection shell	Resolution: 2.06→2.11 Å / Num. unique obs: 2323 / CC_1/2: 0.54

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MIR / Resolution: 2.06→43.704 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.95 / SU B: 3.321 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2361	1603	5.002 %
R_work	0.2183	30444	-
all	0.219	-	-
obs	-	32047	99.956 %

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: 42.866 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.157 Å²	0 Å²	0 Å²
2-	-	-11.152 Å²	-0 Å²
3-	-	-	7.995 Å²

Refinement step

Cycle: LAST / Resolution: 2.06→43.704 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3722	0	44	218	3984

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	3828
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3354
X-RAY DIFFRACTION	r_angle_refined_deg	1.081	1.638	5182
X-RAY DIFFRACTION	r_angle_other_deg	1.349	1.571	7719
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.602	5	491
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.161	24.176	170
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.756	15	596
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.033	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.051	0.2	531
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	4313
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	786
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	597
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	2945
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	1862
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.072	0.2	1811
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.126	0.2	130
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.168	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	58
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.121	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	6.673	16.186	1967
X-RAY DIFFRACTION	r_mcbond_other	6.655	16.181	1966
X-RAY DIFFRACTION	r_mcangle_it	7.733	21.855	2457
X-RAY DIFFRACTION	r_mcangle_other	7.733	21.86	2458
X-RAY DIFFRACTION	r_scbond_it	6.885	16.497	1861
X-RAY DIFFRACTION	r_scbond_other	6.883	16.501	1862
X-RAY DIFFRACTION	r_scangle_it	8.228	22.002	2725
X-RAY DIFFRACTION	r_scangle_other	8.227	22.006	2726
X-RAY DIFFRACTION	r_lrange_it	10.272	92.533	15958
X-RAY DIFFRACTION	r_lrange_other	10.272	92.533	15959

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 (%)
2.06-2.113	0.279	116	0.254	2203	X-RAY DIFFRACTION	99.7849
2.113-2.171	0.297	114	0.268	2163	X-RAY DIFFRACTION	100
2.171-2.234	0.331	109	0.261	2079	X-RAY DIFFRACTION	100
2.234-2.302	0.281	108	0.239	2042	X-RAY DIFFRACTION	100
2.302-2.378	0.301	105	0.26	1988	X-RAY DIFFRACTION	100
2.378-2.461	0.29	101	0.251	1929	X-RAY DIFFRACTION	100
2.461-2.554	0.278	97	0.253	1847	X-RAY DIFFRACTION	100
2.554-2.657	0.283	95	0.241	1799	X-RAY DIFFRACTION	100
2.657-2.775	0.273	91	0.226	1731	X-RAY DIFFRACTION	100
2.775-2.91	0.247	85	0.232	1615	X-RAY DIFFRACTION	99.9412
2.91-3.067	0.251	84	0.231	1588	X-RAY DIFFRACTION	99.9402
3.067-3.252	0.255	78	0.222	1489	X-RAY DIFFRACTION	99.8725
3.252-3.475	0.265	73	0.219	1395	X-RAY DIFFRACTION	99.9319
3.475-3.751	0.217	70	0.217	1314	X-RAY DIFFRACTION	99.9278
3.751-4.106	0.222	64	0.193	1219	X-RAY DIFFRACTION	99.9221
4.106-4.586	0.186	58	0.162	1108	X-RAY DIFFRACTION	99.9143
4.586-5.286	0.185	52	0.179	988	X-RAY DIFFRACTION	100
5.286-6.45	0.239	45	0.246	849	X-RAY DIFFRACTION	100
6.45-9.024	0.21	35	0.218	679	X-RAY DIFFRACTION	100
9.024-43.704	0.157	23	0.227	419	X-RAY DIFFRACTION	99.7743

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Protein , 1 types, 1 molecules AAA

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Non-polymers , 5 types, 225 molecules

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