PDB-3l7m: Structure of the Wall Teichoic Acid Polymerase TagF, H548A

ID or keywords:

Entry

Database: PDB / ID: 3l7m

Title

Structure of the Wall Teichoic Acid Polymerase TagF, H548A

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: 2.85 Å

Authors

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

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	3l7m.cif.gz	713.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3l7m.ent.gz	592.7 KB	Display	PDB format
PDBx/mmJSON format	3l7m.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3l7m_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	3l7m_full_validation.pdf.gz	1.2 MB	Display
Data in XML	3l7m_validation.xml.gz	62.7 KB	Display
Data in CIF	3l7m_validation.cif.gz	83 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l7/3l7m ftp://data.pdbj.org/pub/pdb/validation_reports/l7/3l7m	HTTPS FTP

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Related structure data

Related structure data	3l7iSC 3l7jC 3l7kC 3l7lC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3l7j-d 3l7i-d 3l7l-d 3l7k-d 6mfp-1 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

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

1

Idetical with deposited unit
defined by author&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)	223.510, 223.510, 101.760
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: 86968.070 Da / Num. of mol.: 4 / Fragment: TagF / Mutation: H584A 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-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 18 / 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: 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	Density Matthews: 1.83 Å³/Da / Density % sol: 32.66 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 1.75M ammonium phosphate, pH 7.8, 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: 0.9795 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: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.85→50 Å / Num. all: 537195 / Num. obs: 482401 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / R_merge(I) obs: 0.064 / R_sym value: 0.064 / Net I/σ(I): 25.9
Reflection shell	Resolution: 2.85→3 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.582 / Mean I/σ(I) obs: 1.4 / R_sym value: 0.582 / % possible all: 59.7

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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: 2.85→19.943 Å / SU ML: 0.36 / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2513	2715	5 %	random
R_work	0.1911	-	-	-
obs	0.1941	54256	89.95 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.807 Å² / k_sol: 0.285 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.85→19.943 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13836	0	98	8	13942

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	14261
X-RAY DIFFRACTION	f_angle_d	1.168	19271
X-RAY DIFFRACTION	f_dihedral_angle_d	20.501	5286
X-RAY DIFFRACTION	f_chiral_restr	0.08	1962
X-RAY DIFFRACTION	f_plane_restr	0.004	2472

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 (%)
2.85-2.9017	0.3636	85	0.3322	1591	X-RAY DIFFRACTION	54
2.9017-2.9573	0.3527	93	0.3263	1773	X-RAY DIFFRACTION	60
2.9573-3.0175	0.3508	102	0.3043	1938	X-RAY DIFFRACTION	65
3.0175-3.0829	0.3686	113	0.2936	2143	X-RAY DIFFRACTION	72
3.0829-3.1543	0.3284	123	0.2858	2342	X-RAY DIFFRACTION	79
3.1543-3.2329	0.3357	136	0.2838	2562	X-RAY DIFFRACTION	86
3.2329-3.3199	0.3006	145	0.2686	2753	X-RAY DIFFRACTION	92
3.3199-3.4171	0.3327	155	0.2611	2953	X-RAY DIFFRACTION	99
3.4171-3.5268	0.2944	157	0.2525	2985	X-RAY DIFFRACTION	100
3.5268-3.6521	0.2773	158	0.2189	2993	X-RAY DIFFRACTION	100
3.6521-3.7974	0.2367	158	0.1998	3002	X-RAY DIFFRACTION	100
3.7974-3.9689	0.2783	158	0.1932	3003	X-RAY DIFFRACTION	100
3.9689-4.1764	0.2762	158	0.1743	3012	X-RAY DIFFRACTION	100
4.1764-4.4354	0.2229	160	0.1563	3038	X-RAY DIFFRACTION	100
4.4354-4.7735	0.1917	159	0.1414	3015	X-RAY DIFFRACTION	100
4.7735-5.2459	0.2048	160	0.1375	3039	X-RAY DIFFRACTION	100
5.2459-5.987	0.2239	162	0.1457	3077	X-RAY DIFFRACTION	100
5.987-7.4763	0.217	163	0.1657	3093	X-RAY DIFFRACTION	100
7.4763-19.9433	0.2029	170	0.1564	3229	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	1.7554	-1.7939	0.158	0.9211	-0.1828	0.595	-0.2566	0.0393	0.2796	0.1475	0.0883	-0.3903	-0.2076	0.0675	0.1458	0.6749	-0.0146	-0.1024	0.6147	-0.1396	0.7143	-65.6956	83.1378	-2.9142
2		0.2001	0.3365	1.1944	1.9406	0.384	1.7219	0.2204	-0.2702	-0.1377	0.6851	-0.2078	-0.1998	0.1271	-0.6786	-0.0498	0.8941	-0.0203	-0.0362	0.9047	-0.0132	0.7025
3		2.4031	-2.0015	1.1028	0.0377	-1.0084	2.6747	-0.4105	-0.0013	0.5539	0.2059	0.3189	-0.2729	-0.588	0.275	0.1256	0.9482	0.0492	-0.0396	0.7194	-0.0478	0.8658
4		0.5293	-0.6614	1.8877	-2.1073	-2.6944	2.1833	-1.4666	0.0741	0.6412	0.1157	0.4834	-0.393	-0.8711	-0.1114	0.5426	1.0248	-0.035	-0.1482	0.5636	-0.2047	0.9524
5		1.3717	0.2839	-0.4198	1.7066	0.2285	0.86	-0.1781	-0.2325	-0.1628	-0.3724	0.1149	0.1763	0.0498	0.0278	0.0955	0.7369	0.1052	-0.0358	0.7079	-0.0293	0.6681
6		0.7423	-0.5609	0.0017	1.8604	-0.7384	0.3468	-0.1855	-1.065	-0.1101	0.7724	0.3448	0.5362	-0.1476	-0.838	-0.1277	0.835	0.1168	0.0877	1.1443	0.0376	0.6365
7		2.1041	2.327	-0.1187	1.5431	0.4312	1.4352	-0.1178	-0.0886	-0.3556	-0.0433	0.0394	-0.4405	0.2163	-0.0008	0.097	0.6121	0.0202	0.0676	0.6261	-0.0271	0.768
8		1.0741	0.1794	-0.7712	2.2258	0.0636	1.0082	-0.0396	0.2121	0.1706	-0.0059	0.0612	-0.2328	-0.2608	-0.499	-0.0022	0.7112	0.0103	0.0063	0.8757	-0.0129	0.715
9		2.8397	1.4934	-0.2594	1.2648	-0.522	1.6199	-0.827	0.0039	-0.706	-0.1573	0.5429	0.2333	0.5854	0.0967	0.3883	0.8291	-0.0896	0.1898	0.6352	-0.0619	0.9083
10		0.1614	-0.7758	0.1913	1.7896	-1.1737	0.5523	0.3201	-0.2487	0.6299	1.3112	-0.8104	-0.0191	-0.5757	-0.1897	0.2108	1.3582	-0.2605	0.1435	0.8927	-0.2118	1.0224
11		2.4723	-0.1425	-0.1568	1.5759	-0.1262	1.0615	-0.4951	0.1749	0.1071	0.3575	0.4504	0.1042	-0.0103	-0.1646	0.0919	0.7128	-0.093	0.0367	0.6452	-0.0177	0.6676
12		0.812	0.3938	0.5044	1.0949	-0.6319	0.6212	-0.134	0.7944	0.1349	-0.4707	0.2225	0.3358	0.1029	-0.6574	-0.0248	0.8183	-0.1354	-0.0434	0.9152	-0.0878	0.6641
13		2.065	-1.9811	-0.0383	1.3059	-0.1188	1.0317	-0.4089	-0.1799	-0.4458	0.2965	0.2356	0.6849	0.3261	0.0721	0.1505	0.7726	0.0404	0.1348	0.608	0.1299	0.8322
14		0.2574	0.511	-0.9942	2.2361	0.0991	1.8775	0.2694	-0.4491	0.2062	0.4963	-0.1502	-0.0185	-0.6534	0.8332	-0.1362	0.8548	-0.0133	-0.0022	0.8726	-0.0004	0.6497
15		2.1699	0.3495	-0.0783	0.2573	-1.5796	0.8592	-0.4808	-0.4587	-0.5569	0.4801	0.0932	-0.003	0.2724	-0.0327	0.2271	0.9435	0.1183	0.1157	0.8198	0.2599	0.734
16		0.2169	-0.1769	-0.7287	2.0358	0.3791	2.3818	0.1496	-0.024	0.3012	-0.2259	-0.6646	-0.4334	-0.6859	-0.3159	0.1884	1.235	0.0571	0.114	1.041	0.1186	1.1384
17		1.733	-0.619	-0.0999	1.4962	0.4037	0.3843	-0.2031	-0.3383	0.0323	-0.4369	0.232	-0.1367	-0.1479	-0.1159	-0.0496	0.8846	0.0693	0.0688	0.8293	0.0971	0.6677
18		1.06	-1.3261	0.2042	2.0714	0.9623	-0.1272	-0.2004	-0.9845	0.1676	0.7557	0.2698	-0.4839	0.1644	0.8565	-0.0411	0.8496	0.1796	-0.243	1.2761	0.0343	0.5975
19		2.8451	1.9679	0.0993	1.4284	-0.5036	1.239	-0.2815	0.0601	0.2798	-0.1048	0.1511	0.4217	-0.2646	0.0543	0.125	0.7193	-0.0053	-0.0996	0.6661	0.0411	0.8792
20		1.6992	-0.6962	-0.231	-0.0512	-0.1408	1.3103	-1.3267	0.3023	0.0295	0.4043	0.6003	-0.1141	0.7493	-0.3119	0.6714	1.0287	0.1398	0.1008	1.5574	-0.2388	0.859
21		3.3166	0.7006	1.0662	0.8923	-0.46	1.9945	-0.2636	0.425	0.424	-0.3082	0.0879	0.3805	-0.2754	0.2178	0.0849	0.7063	-0.0939	-0.0619	0.7257	0.1281	0.7308
22		1.7044	1.293	-0.6137	1.2244	-0.6903	1.867	-0.0146	-0.2214	-0.148	-0.7859	0.0259	0.1594	0.6844	-0.4095	0.1677	1.2796	-0.1142	0.0257	1.1619	0.0225	1.1349
23		1.8943	0.8868	-0.3544	1.7848	-0.3351	1.0987	-0.1457	0.1872	-0.0786	0.3957	0.177	0.0152	0.0025	-0.1561	-0.084	0.7807	-0.0503	-0.1064	0.7119	0.0262	0.7427
24		1.2249	0.6925	0.7266	1.344	0.0459	0.446	-0.3204	1.2956	-0.1339	-0.6357	0.3376	-0.2095	0.07	0.7451	0.0037	0.8941	-0.2241	0.1041	1.1759	0.0215	0.622

Refinement TLS group

Selection details: chain D and resid 653:724)

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