PDB-8p1x: TarM(Se)_G117R-UDP-glucose

ID or keywords:

Entry

Database: PDB / ID: 8p1x

Title

TarM(Se)_G117R-UDP-glucose

Components

TarM(Se)

Keywords

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

Function / homology

TRIETHYLENE GLYCOL / PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE

Function and homology information

Biological species

Staphylococcus epidermidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 2.03 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	May 13, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8p1x.cif.gz	128.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8p1x.ent.gz		Display	PDB format
PDBx/mmJSON format	8p1x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p1/8p1x ftp://data.pdbj.org/pub/pdb/validation_reports/p1/8p1x	HTTPS FTP

-
Related structure data

Related structure data	7qd7C 7qh9C 7qntC 8p20C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

AAA: TarM(Se)

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	58.650, 88.730, 98.050
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 1 molecules AAA

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

-
Non-polymers , 7 types, 300 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₂O₁₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.48 %
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)2SO4. PH range: 6.2-8.1

-
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	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.03→49.03 Å / Num. obs: 33765 / % possible obs: 100 % / Redundancy: 13.2 % / CC_1/2: 0.999 / Net I/σ(I): 15.64
Reflection shell	Resolution: 2.03→2.08 Å / Num. unique obs: 2443 / CC_1/2: 0.52 / % possible all: 100

-
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: 2.03→49.025 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.937 / SU B: 3.068 / SU ML: 0.089 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2381	1689	5.002 %
R_work	0.2012	32075	-
all	0.203	-	-
obs	-	33764	99.976 %

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: 34.271 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.034 Å²	0 Å²	0 Å²
2-	-	-0.139 Å²	-0 Å²
3-	-	-	-3.895 Å²

Refinement step

Cycle: LAST / Resolution: 2.03→49.025 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3847	0	81	290	4218

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	3993
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3591
X-RAY DIFFRACTION	r_angle_refined_deg	1.143	1.642	5395
X-RAY DIFFRACTION	r_angle_other_deg	1.341	1.573	8304
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.562	5	491
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.614	23.915	189
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.39	15	684
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.389	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	546
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4391
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	811
X-RAY DIFFRACTION	r_nbd_refined	0.179	0.2	695
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	3270
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	1944
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	1809
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	204
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.233	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.168	0.2	55
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.178	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	4.674	12.42	1967
X-RAY DIFFRACTION	r_mcbond_other	4.654	12.417	1966
X-RAY DIFFRACTION	r_mcangle_it	5.632	16.748	2457
X-RAY DIFFRACTION	r_mcangle_other	5.632	16.751	2458
X-RAY DIFFRACTION	r_scbond_it	4.948	12.893	2026
X-RAY DIFFRACTION	r_scbond_other	4.947	12.892	2027
X-RAY DIFFRACTION	r_scangle_it	6.093	17.157	2938
X-RAY DIFFRACTION	r_scangle_other	6.092	17.156	2939
X-RAY DIFFRACTION	r_lrange_it	8.052	70.998	16720
X-RAY DIFFRACTION	r_lrange_other	8.052	70.996	16721

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 (%)
2.03-2.083	0.314	122	0.265	2315	X-RAY DIFFRACTION	99.877
2.083-2.14	0.312	119	0.237	2257	X-RAY DIFFRACTION	99.9579
2.14-2.201	0.301	117	0.247	2224	X-RAY DIFFRACTION	100
2.201-2.269	0.246	114	0.226	2168	X-RAY DIFFRACTION	99.9562
2.269-2.343	0.261	110	0.23	2091	X-RAY DIFFRACTION	100
2.343-2.425	0.264	106	0.219	2016	X-RAY DIFFRACTION	100
2.425-2.517	0.287	102	0.208	1934	X-RAY DIFFRACTION	100
2.517-2.619	0.238	99	0.203	1884	X-RAY DIFFRACTION	100
2.619-2.735	0.257	96	0.209	1815	X-RAY DIFFRACTION	99.9477
2.735-2.868	0.274	92	0.222	1746	X-RAY DIFFRACTION	100
2.868-3.023	0.283	87	0.218	1652	X-RAY DIFFRACTION	100
3.023-3.205	0.241	82	0.204	1570	X-RAY DIFFRACTION	100
3.205-3.426	0.231	78	0.203	1485	X-RAY DIFFRACTION	100
3.426-3.699	0.251	73	0.188	1388	X-RAY DIFFRACTION	100
3.699-4.049	0.194	68	0.169	1276	X-RAY DIFFRACTION	99.9257
4.049-4.524	0.179	61	0.156	1172	X-RAY DIFFRACTION	100
4.524-5.216	0.16	55	0.156	1042	X-RAY DIFFRACTION	100
5.216-6.37	0.246	47	0.22	894	X-RAY DIFFRACTION	100
6.37-8.934	0.212	38	0.21	709	X-RAY DIFFRACTION	99.8663
8.934-49.025	0.312	23	0.221	437	X-RAY DIFFRACTION	100

-
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

-
Protein , 1 types, 1 molecules AAA

-
Non-polymers , 7 types, 300 molecules

-
Details

-
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

-Protein , 1 types, 1 molecules AAA

-Non-polymers , 7 types, 300 molecules

-Details

-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

-
Protein , 1 types, 1 molecules AAA

-
Non-polymers , 7 types, 300 molecules

-
Details

-
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