PDB-3l7k: Structure of the Wall Teichoic Acid Polymerase TagF, H444N + CDPG...

ID or keywords:

Entry

Database: PDB / ID: 3l7k

Title

Structure of the Wall Teichoic Acid Polymerase TagF, H444N + CDPG (15 minute soak)

Components

Teichoic acid biosynthesis protein F

Keywords

STRUCTURAL PROTEIN / GT-B fold / monotopic membrane protein

Function / homology

Function and homology information

teichoic acid poly(glycerol phosphate) polymerase / CDP-glycerol glycerophosphotransferase activity / teichoic acid biosynthetic process / cell wall organization / plasma membrane
Similarity search - Function

Biological species

Staphylococcus epidermidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Strynadka, N.C.J. / Lovering, A.L.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structure of the bacterial teichoic acid polymerase TagF provides insights into membrane association and catalysis.
Authors: Lovering, A.L. / Lin, L.Y. / Sewell, E.W. / Spreter, T. / Brown, E.D. / Strynadka, N.C.

History

Deposition	Dec 28, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 28, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 13, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3l7k.cif.gz	711.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3l7k.ent.gz	587 KB	Display	PDB format
PDBx/mmJSON format	3l7k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3l7k_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	3l7k_full_validation.pdf.gz	1.4 MB	Display
Data in XML	3l7k_validation.xml.gz	63.6 KB	Display
Data in CIF	3l7k_validation.cif.gz	84.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l7/3l7k ftp://data.pdbj.org/pub/pdb/validation_reports/l7/3l7k	HTTPS FTP

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Related structure data

Related structure data	3l7iSC 3l7jC 3l7lC 3l7mC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3l7l-d 3l7i-d 3l7j-d 3l7m-d 6kdy-d 6epz-d 6eq8-d 4uoo-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (3) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1)

Deposited unit

A: Teichoic acid biosynthesis protein F

B: Teichoic acid biosynthesis protein F

C: Teichoic acid biosynthesis protein F

D: Teichoic acid biosynthesis protein F

hetero molecules

351 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

2

A: Teichoic acid biosynthesis protein F

B: Teichoic acid biosynthesis protein F

hetero molecules

defined by author&software
175 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Teichoic acid biosynthesis protein F

D: Teichoic acid biosynthesis protein F

hetero molecules

defined by author&software
175 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	222.040, 222.040, 100.910
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Teichoic acid biosynthesis protein F Mass: 87011.102 Da / Num. of mol.: 4 / Fragment: TagF / Mutation: H444N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: RP62A / Gene: SERP1960, tagF / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HLM5

#1: Protein

Teichoic acid biosynthesis protein F

Mass: 87011.102 Da / Num. of mol.: 4 / Fragment: TagF / Mutation: H444N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Staphylococcus epidermidis (bacteria) / Strain: RP62A / Gene: SERP1960, tagF / Plasmid: pET28b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HLM5

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Non-polymers , 6 types, 40 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID Mass: 292.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₂O₈
#5: Chemical	ChemComp-C2G / [CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER / CYTIDINE 5'-DIPHOSPHOGLYCEROL Mass: 477.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₁N₃O₁₃P₂
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jun 1, 2009
Radiation	Monochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.95→50 Å / Num. obs: 353235 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / R_merge(I) obs: 0.089 / R_sym value: 0.089 / Net I/σ(I): 15.6
Reflection shell	Resolution: 2.95→3.11 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.62 / Mean I/σ(I) obs: 1.4 / Num. unique all: 353235 / R_sym value: 0.62 / % possible all: 92.9

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
SHELXS		phasing
PHENIX	(phenix.refine)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3L7I

3l7i

Resolution: 3.1→19.857 Å / SU ML: 0.4 / σ(F): 1.99 / σ(I): 0 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2518	2285	4.99 %	random
R_work	0.1896	-	-	-
obs	0.1927	45754	99.32 %	-
all	-	353235	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 37.631 Å² / k_sol: 0.267 e/Å³

Refinement step

Cycle: LAST / Resolution: 3.1→19.857 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13709	0	126	8	13843

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	14155
X-RAY DIFFRACTION	f_angle_d	1.156	19129
X-RAY DIFFRACTION	f_dihedral_angle_d	20.391	5273
X-RAY DIFFRACTION	f_chiral_restr	0.077	1944
X-RAY DIFFRACTION	f_plane_restr	0.005	2451

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 (%)
3.1001-3.1672	0.3539	135	0.3258	2583	X-RAY DIFFRACTION	95
3.1672-3.2406	0.3706	136	0.3032	2570	X-RAY DIFFRACTION	96
3.2406-3.3213	0.313	140	0.2799	2667	X-RAY DIFFRACTION	99
3.3213-3.4106	0.2992	142	0.2639	2691	X-RAY DIFFRACTION	100
3.4106-3.5105	0.3084	142	0.2522	2695	X-RAY DIFFRACTION	100
3.5105-3.6231	0.3219	143	0.225	2715	X-RAY DIFFRACTION	100
3.6231-3.7518	0.2523	143	0.2105	2719	X-RAY DIFFRACTION	100
3.7518-3.9009	0.3049	141	0.1972	2692	X-RAY DIFFRACTION	100
3.9009-4.077	0.2509	143	0.1845	2714	X-RAY DIFFRACTION	100
4.077-4.2899	0.2269	142	0.173	2718	X-RAY DIFFRACTION	100
4.2899-4.5556	0.2213	144	0.1571	2731	X-RAY DIFFRACTION	100
4.5556-4.9025	0.2103	143	0.1436	2724	X-RAY DIFFRACTION	100
4.9025-5.3869	0.2271	144	0.1473	2759	X-RAY DIFFRACTION	100
5.3869-6.146	0.2047	146	0.1515	2764	X-RAY DIFFRACTION	100
6.146-7.6685	0.2429	149	0.1648	2820	X-RAY DIFFRACTION	100
7.6685-19.857	0.2008	152	0.1569	2907	X-RAY DIFFRACTION	100

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	Method	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	refined	2.1679	-1.1777	0.1601	0.2578	-0.3437	0.4125	-0.1653	0.1445	0.1721	0.0213	0.0252	-0.2064	-0.2426	-0.036	0.1256	0.8866	0.0035	-0.0589	0.8707	-0.1146	0.8065	-95.3795	80.7081	-14.5218
2		2.9386	0.4952	-0.0526	0.1801	0.8028	-1.5821	0.5582	-0.1078	0.2219	-0.0815	-1.5155	0.243	0.4769	1.3036	0.8856	1.3186	-0.1651	0.0135	2.5448	0.906	1.9733
3		2.1795	-0.6012	0.7197	2.226	-0.6315	2.0418	-0.1178	-0.3082	0.0915	0.3395	0.1607	-0.082	0.0511	-0.1386	-0.0617	0.876	0.0178	0.0401	0.8234	-0.0222	0.7046
4		1.5759	0.2308	0.0396	3.0626	0.0544	0.4219	-0.2164	-0.2576	-0.2491	-0.253	0.3156	0.1851	-0.2076	-0.0206	-0.028	0.8843	0.0535	-0.0608	0.8157	-0.0097	0.6987
5		6.5427	-2.5523	0.8764	8.4823	-3.8954	8.2386	0.5428	-0.4579	0.2773	-0.9773	-2.0841	-2.0785	0.1931	-0.7364	0.8287	1.3354	-0.0243	-0.0691	1.0557	-0.2141	1.272
6		0.6841	-0.5571	-0.2833	1.6696	-0.6055	-0.444	0.1029	-0.8524	-0.241	0.7822	0.2318	0.5719	0.1262	-0.7431	-0.1267	0.864	0.021	0.1093	1.111	-0.051	0.671
7		3.4258	1.9981	0.5316	1.9338	0.7726	1.2451	-0.1703	-0.1053	-0.2885	0.0095	0.0168	-0.3528	0.2277	0.0799	0.1413	0.7789	0.0177	0.0591	0.8509	-0.0397	0.9933
8		8.0015	-5.7409	-3.763	8.8638	-1.3113	2.3161	-1.0104	0.8129	-0.1382	1.5145	-0.5797	0.3207	-0.618	-0.9108	1.3541	1.3102	0.1833	-0.2131	1.705	0.1333	0.8659
9		2.9108	0.0927	-1.1138	1.2676	-0.8237	1.729	-0.0913	0.3252	0.0292	-0.1311	0.0456	-0.1683	0.0832	-0.1932	0.0725	0.8832	-0.0558	-0.0284	0.8957	-0.0644	0.7963
10		0.8161	0.5479	0.1287	5.0736	0.3848	0.511	0.8937	0.4397	1.3034	-0.6416	-0.7983	0.1154	-0.0454	0.0652	-0.166	1.002	-0.071	-0.0547	0.9902	-0.123	1.3926
11		1.901	-0.9987	0.6457	2.2872	0.5526	0.906	-0.5155	0.1869	0.2615	0.4159	0.4129	-0.0214	0.1343	0.165	0.1259	0.9622	-0.0711	0.034	0.8381	0.0023	0.7783
12		-0.1698	0.1292	0.1078	1.4852	0.1522	0.859	0.1018	0.5195	0.076	-0.4156	-0.0173	0.3643	0.0339	-0.5721	-0.0972	0.966	-0.08	-0.0855	1.188	0.07	0.8793
13		2.3296	-1.8792	-0.0451	1.4533	0.4035	0.9553	-0.2494	-0.0571	-0.1216	0.2577	0.0709	0.3725	0.3243	0.1417	0.137	0.9528	0.0272	0.0928	0.9695	0.097	0.9923
14		0.4621	0.0992	0.2661	1.1379	-1.2753	0.6611	-0.0331	-0.4352	0.0839	0.6726	0.3321	0.1621	-0.3914	0.2816	-0.1821	1.0417	0.0199	0.0659	1.0772	-0.1108	0.6613
15		3.8337	-0.5527	-0.9469	1.1365	-1.8176	0.5626	-0.2362	-0.458	-0.6584	-0.1564	0.328	0.1765	0.0519	-0.2015	-0.0416	1.0036	0.0215	-0.0077	1.0043	0.2067	0.8706
16		-4.6769	3.4294	-1.294	5.7481	-0.1588	6.2645	-0.3392	-0.2918	-0.8501	-0.3213	-0.7193	-1.2877	-0.7464	-0.6169	0.2905	1.6253	-0.147	0.2878	2.0019	0.1309	1.8577
17		3.2067	-0.5346	1.1447	2.8243	0.0631	-0.2797	-0.3164	-0.3859	0.366	-0.413	0.3345	-0.1782	0.2261	-0.0838	0.0283	1.0743	0.0275	0.1038	0.9325	0.1014	0.7456
18		1.3203	-0.0633	-0.1258	1.6271	0.834	-0.7691	0.2601	-0.5906	-0.0402	0.6099	0.0571	-0.4117	-0.1452	0.6525	-0.1334	1.0113	0.1765	-0.2198	1.4452	0.0333	0.8116
19		3.4566	1.3101	-0.1115	0.3207	-0.2849	0.6963	-0.2345	-0.0595	0.2483	-0.1034	0.0643	0.2639	-0.2936	0.0436	0.204	0.8587	-0.07	-0.1024	0.7727	0.0001	0.9749
20		1.3509	0.3107	0.3812	3.0464	-0.1864	1.1462	-0.3907	0.3648	0.0705	-0.6614	0.3235	0.4259	0.4935	0.4155	-0.0325	0.9742	0.0349	-0.0173	0.9929	-0.0606	0.8915
21		3.564	-0.7241	-0.0412	0.048	-0.4718	2.06	-0.7897	0.1697	0.7068	0.1794	0.2169	0.2579	-0.3967	-0.301	0.4964	1.0546	-0.1238	-0.1746	0.8719	0.0675	1.1841
22		5.2962	1.6443	1.9187	1.8633	3.4514	-1.9425	0.062	0.7117	1.1296	-3.4582	-0.5494	0.9535	-0.2682	1.7719	0.0741	1.6484	0.0745	0.0222	0.9749	0.2241	1.0643
23		3.49	-0.1518	2.3333	2.6225	-0.6892	0.8746	-0.3569	0.6898	-0.3349	-0.1783	0.261	-0.3082	-0.2038	0.315	0.1467	1.0383	-0.2047	0.0977	1.1533	0.023	0.9106
24		2.0254	-0.5529	-1.2246	1.8343	-0.5359	1.0716	0.1781	1.3706	0.0033	0.2135	-0.045	0.6981	0.1561	0.0073	-0.0844	1.0113	-0.1233	-0.198	1.1731	0.3604	0.9952

Refinement TLS group

Selection details: chain D and resid 712:724)

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