PDB-3l7j: Structure of the Wall Teichoic Acid Polymerase TagF, H444N variant

ID or keywords:

Entry

Database: PDB / ID: 3l7j

Title

Structure of the Wall Teichoic Acid Polymerase TagF, H444N variant

Components

Teichoic acid biosynthesis protein F

Keywords

STRUCTURAL PROTEIN / GT-B / 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: 2.81 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	3l7j.cif.gz	714 KB	Display	PDBx/mmCIF format
PDB format	pdb3l7j.ent.gz	591.8 KB	Display	PDB format
PDBx/mmJSON format	3l7j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3l7j_validation.pdf.gz	504 KB	Display	wwPDB validaton report
Full document	3l7j_full_validation.pdf.gz	548.8 KB	Display
Data in XML	3l7j_validation.xml.gz	60.4 KB	Display
Data in CIF	3l7j_validation.cif.gz	80.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l7/3l7j ftp://data.pdbj.org/pub/pdb/validation_reports/l7/3l7j	HTTPS FTP

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Related structure data

Related structure data	3l7iSC 3l7kC 3l7lC 3l7mC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3l7l-d 3l7i-d 3l7m-d 3l7k-d 4uoo-d 6eq8-d 6kdy-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

350 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)	223.600, 223.600, 100.570
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#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
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 20 / 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	Density Matthews: 1.81 Å³/Da / Density % sol: 31.89 %
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: 2.81→50 Å / Num. obs: 450040 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / R_merge(I) obs: 0.089 / R_sym value: 0.089 / Net I/σ(I): 16.5
Reflection shell	Resolution: 2.81→3 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.581 / Mean I/σ(I) obs: 1.6 / R_sym value: 0.581 / % possible all: 91.4

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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: 3L7I

3l7i

Resolution: 2.81→19.796 Å / SU ML: 0.41 / σ(F): 1.99 / σ(I): 0 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2458	3046	5 %	random
R_work	0.1974	-	-	-
obs	0.1998	60921	97.89 %	-
all	-	450040	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 28.541 Å² / k_sol: 0.266 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.81→19.796 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13878	0	72	20	13970

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	14268
X-RAY DIFFRACTION	f_angle_d	1.224	19284
X-RAY DIFFRACTION	f_dihedral_angle_d	20.139	5264
X-RAY DIFFRACTION	f_chiral_restr	0.084	1964
X-RAY DIFFRACTION	f_plane_restr	0.005	2482

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 (%)
2.81-2.8538	0.3695	116	0.3526	2217	X-RAY DIFFRACTION	84
2.8538-2.9004	0.3524	122	0.3352	2306	X-RAY DIFFRACTION	87
2.9004-2.9503	0.3953	127	0.3348	2427	X-RAY DIFFRACTION	91
2.9503-3.0038	0.3546	131	0.3112	2477	X-RAY DIFFRACTION	95
3.0038-3.0613	0.3468	136	0.303	2589	X-RAY DIFFRACTION	97
3.0613-3.1236	0.3571	139	0.2961	2644	X-RAY DIFFRACTION	100
3.1236-3.1912	0.3469	140	0.2662	2659	X-RAY DIFFRACTION	100
3.1912-3.2651	0.3304	141	0.2591	2669	X-RAY DIFFRACTION	100
3.2651-3.3464	0.2733	140	0.2538	2659	X-RAY DIFFRACTION	100
3.3464-3.4364	0.3236	139	0.2347	2654	X-RAY DIFFRACTION	100
3.4364-3.537	0.254	140	0.2244	2663	X-RAY DIFFRACTION	100
3.537-3.6505	0.2637	140	0.2096	2657	X-RAY DIFFRACTION	100
3.6505-3.7801	0.2522	142	0.1983	2682	X-RAY DIFFRACTION	100
3.7801-3.9303	0.25	141	0.1909	2680	X-RAY DIFFRACTION	100
3.9303-4.1077	0.2153	140	0.1643	2674	X-RAY DIFFRACTION	100
4.1077-4.3221	0.2163	143	0.154	2703	X-RAY DIFFRACTION	100
4.3221-4.5898	0.1723	142	0.1439	2695	X-RAY DIFFRACTION	100
4.5898-4.9391	0.2252	142	0.1406	2699	X-RAY DIFFRACTION	100
4.9391-5.4268	0.197	143	0.1456	2722	X-RAY DIFFRACTION	100
5.4268-6.1909	0.2111	144	0.1509	2735	X-RAY DIFFRACTION	100
6.1909-7.7222	0.1949	147	0.1735	2785	X-RAY DIFFRACTION	100
7.7222-19.7967	0.2057	151	0.1618	2879	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	1.865	-0.9662	-0.176	0.8376	-0.0246	0.9457	-0.1279	0.1494	0.1236	0.1611	-0.0103	-0.3308	-0.2341	0.0362	0.1206	0.6842	-0.0221	-0.0642	0.6412	-0.0931	0.672	-65.5603	82.874	-3.0523
2		1.3509	0.269	0.4593	2.0207	1.7556	0.9346	0.2756	-0.5172	-0.0081	-0.5886	-1.6381	-0.2256	-0.0073	0.4183	0.9083	1.0944	0.2185	-0.1754	2.5752	0.6485	1.4061
3		1.8227	0.0734	1.215	2.5221	-0.4552	2.6322	-0.3247	-0.4204	0.1358	0.7641	0.2865	-0.2758	-0.2832	-0.2123	0.0247	0.7148	0.0143	0.0173	0.6341	-0.1063	0.5681
4		0.071	1.2276	-0.6063	2.6796	1.0888	1.603	0.245	0.0737	-1.0412	0.2251	-0.1518	1.8441	-0.0921	0.3103	0.3878	1.0827	0.0171	-0.0673	0.8224	-0.1744	0.7439
5		1.4333	0.4621	-1.5773	3.1943	0.5094	1.2878	-0.1778	-0.1791	-0.2403	-0.3647	0.2196	0.24	-0.0316	0.1567	0.0025	0.7526	0.0824	-0.0639	0.672	0.0241	0.6649
6		0.4862	-0.443	-0.0277	1.4189	-1.1568	0.6401	-0.1401	-0.7794	-0.1181	0.6683	0.3999	0.4179	-0.1034	-0.7688	-0.1218	0.8034	0.15	0.0771	1.056	-0.0763	0.6851
7		2.0928	1.8223	0.3614	1.2892	0.8471	1.3015	-0.1381	-0.1438	-0.1608	0.0586	0.0059	-0.3876	0.2662	0.0777	0.0874	0.5725	0.027	0.0246	0.5623	-0.0537	0.7727
8		0.6035	-1.5518	-2.9937	4.8938	-1.7247	2.7776	0.1503	0.7341	-0.1854	0.469	-1.8587	0.5705	-0.6044	0.9461	0.9815	1.3421	0.0621	-0.2854	2.0115	0.2583	1.2239
9		2.9661	0.5934	-1.1569	1.1527	-0.9697	2.4956	-0.3328	0.2613	-0.0398	-0.1617	0.1872	-0.2718	0.1672	-0.1946	0.1275	0.6398	0.004	-0.0029	0.5827	-0.0965	0.6113
10		4.3877	2.5266	0.7792	5.3155	3.0077	3.0593	-0.1435	-0.3514	0.063	-0.0399	-0.0715	1.6832	0.0741	-0.058	0.6618	2.2985	-0.3298	0.6346	1.3401	-0.1058	1.9551
11		2.7663	0.054	0.8619	2.2182	0.0703	2.0522	-0.3515	0.1057	0.0827	0.3904	0.269	0.0773	-0.1064	-0.0064	0.1055	0.8007	-0.0576	0.0669	0.6658	-0.0408	0.6972
12		1.6069	-0.0959	0.8571	0.892	-0.5114	0.8525	-0.0936	1.0253	-0.0521	-0.4823	0.0612	0.3122	0.0891	-0.7005	0.0634	0.7409	-0.0912	-0.016	0.7914	-0.1202	0.6728
13		1.8638	-1.6841	0.1848	1.1826	-0.5617	1.9427	-0.2685	-0.021	-0.324	0.0375	0.1465	0.5465	0.4278	0.0527	0.1114	0.6974	-0.0041	0.064	0.6454	0.1048	0.8142
14		0.3998	0.5374	-0.1273	1.3191	1.2279	0.7146	0.0579	-0.117	0.0656	0.2109	0.1667	-0.0572	-0.084	0.6073	-0.1867	0.7607	-0.0079	0.0331	0.8642	-0.0323	0.6175
15		3.0266	0.5796	-1.1972	2.0989	0.1733	1.515	-0.436	-0.41	-0.5436	0.2694	0.3469	-0.0471	0.3528	0.0157	0.0358	0.9006	0.1155	0.038	0.7665	0.1958	0.6253
16		-3.6581	2.376	-0.8846	2.755	0.1182	0.7453	0.0567	0.2889	-0.1354	-0.296	-0.009	-1.4097	-0.3636	0.0375	-0.5184	1.4345	-0.1028	0.1668	1.8093	0.0767	1.6739
17		1.8972	-1.1248	0.9977	1.9462	-0.2072	0.264	-0.1775	-0.383	0.2515	-0.294	0.2861	-0.1235	0.0395	-0.1506	-0.0995	0.8161	0.03	0.0732	0.7426	0.0405	0.5356
18		1.4766	-0.6023	0.6448	1.4844	1.1267	-0.6166	-0.0648	-1.0042	0.1681	0.6393	0.3044	-0.373	0.1722	0.7571	-0.1198	0.7371	0.1444	-0.1428	1.1214	0.0321	0.4967
19		2.8744	1.7202	-0.1761	0.6707	-0.8704	0.914	-0.2236	0.0011	0.1727	0.0678	0.0648	0.2191	-0.2801	0.0179	0.166	0.6158	-0.006	-0.0792	0.5985	-0.0023	0.8316
20		-0.155	-1.2283	-0.1685	1.697	-0.6692	1.9052	-1.3529	0.1935	0.4781	0.4362	-1.128	0.6252	-0.8987	-1.8042	1.7438	1.914	-0.2511	-0.0495	2.2191	-0.3699	0.9536
21		2.8247	0.7138	1.4105	1.6777	0.631	1.7434	-0.3033	0.2171	0.249	-0.1314	0.1168	0.2419	-0.0214	0.2534	0.1094	0.6631	-0.0584	-0.0344	0.7003	0.0215	0.7159
22		3.4615	0.9125	-0.6529	2.1982	-0.2399	2.3054	-0.3395	0.2703	-0.1155	0.349	0.3162	-0.0839	0.1588	-0.2012	0.0156	0.7844	-0.0421	-0.1038	0.6231	0.0691	0.6703
23		3.4677	-1.1931	1.9317	-0.8775	-0.0557	-1.0912	-1.2111	2.7857	-1.1908	0.6167	0.2032	1.4068	-0.0267	0.0761	0.7529	1.0619	-0.4279	-0.2808	1.8105	0.0923	1.7767
24		2.5398	1.1248	-0.2469	1.5106	0.1808	-0.3845	-0.4517	1.2919	-0.2614	-0.592	0.4433	-0.2944	-0.1692	0.6285	-0.0164	0.816	-0.1466	0.0849	1.083	0.0046	0.5889

Refinement TLS group

Selection details: chain D and resid 652:724)

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