PDB-3l7l: Structure of the Wall Teichoic Acid Polymerase TagF, H444N + CDPG...

ID or keywords:

Entry

Database: PDB / ID: 3l7l

Title

Structure of the Wall Teichoic Acid Polymerase TagF, H444N + CDPG (30 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: 2.95 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	3l7l.cif.gz	713 KB	Display	PDBx/mmCIF format
PDB format	pdb3l7l.ent.gz	588.8 KB	Display	PDB format
PDBx/mmJSON format	3l7l.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/l7/3l7l ftp://data.pdbj.org/pub/pdb/validation_reports/l7/3l7l	HTTPS FTP

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Related structure data

Related structure data	3l7iSC 3l7jC 3l7kC 3l7mC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3l7i-d 3l7j-d 3l7k-d 3l7m-d 4uoo-d 6kdy-d 6epz-d 6eq8-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)	222.880, 222.880, 100.750
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 , 5 types, 33 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	... ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 4 / 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: 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: 2.95→50 Å / Num. all: 305757 / Num. obs: 303005 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / R_merge(I) obs: 0.099 / R_sym value: 0.099 / Net I/σ(I): 12.4
Reflection shell	Resolution: 3.1→3.27 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.434 / Mean I/σ(I) obs: 1.8 / R_sym value: 0.434 / % possible all: 96.5

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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: 2.95→20.012 Å / SU ML: 0.43 / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2539	2650	5.01 %	random
R_work	0.1931	-	-	-
obs	0.1962	52937	98.68 %	-

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.504 Å² / k_sol: 0.287 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.95→20.012 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13779	0	85	4	13868

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	14190
X-RAY DIFFRACTION	f_angle_d	1.272	19180
X-RAY DIFFRACTION	f_dihedral_angle_d	20.829	5263
X-RAY DIFFRACTION	f_chiral_restr	0.084	1952
X-RAY DIFFRACTION	f_plane_restr	0.005	2465

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 (%)
2.9501-3.0036	0.3579	125	0.3379	2361	X-RAY DIFFRACTION	90
3.0036-3.0612	0.3825	129	0.328	2439	X-RAY DIFFRACTION	92
3.0612-3.1235	0.353	132	0.3249	2503	X-RAY DIFFRACTION	96
3.1235-3.1911	0.3657	137	0.303	2613	X-RAY DIFFRACTION	98
3.1911-3.265	0.3484	140	0.2841	2658	X-RAY DIFFRACTION	100
3.265-3.3463	0.3151	140	0.2641	2651	X-RAY DIFFRACTION	100
3.3463-3.4364	0.2849	140	0.2403	2641	X-RAY DIFFRACTION	100
3.4364-3.5369	0.3065	140	0.2284	2649	X-RAY DIFFRACTION	100
3.5369-3.6504	0.2759	140	0.2088	2652	X-RAY DIFFRACTION	100
3.6504-3.7801	0.2625	140	0.2073	2665	X-RAY DIFFRACTION	100
3.7801-3.9303	0.2748	140	0.1876	2663	X-RAY DIFFRACTION	100
3.9303-4.1077	0.2264	142	0.1689	2674	X-RAY DIFFRACTION	100
4.1077-4.3222	0.2341	140	0.1522	2661	X-RAY DIFFRACTION	100
4.3222-4.59	0.1808	141	0.1446	2703	X-RAY DIFFRACTION	100
4.59-4.9395	0.2055	142	0.1364	2700	X-RAY DIFFRACTION	100
4.9395-5.4275	0.1959	142	0.1494	2699	X-RAY DIFFRACTION	100
5.4275-6.1924	0.2492	143	0.1616	2726	X-RAY DIFFRACTION	100
6.1924-7.7264	0.2244	145	0.181	2764	X-RAY DIFFRACTION	100
7.7264-20.0121	0.238	152	0.1625	2865	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	2.3231	-1.0566	0.1166	1.1403	0.0123	0.8349	-0.1517	0.027	0.1979	0.0813	0.0784	-0.3074	-0.2524	0.0447	0.0635	0.8337	-0.0236	-0.0503	0.7753	-0.1159	0.7697	-95.8355	80.8399	-14.7584
2		3.4618	0.0377	-0.7565	3.1086	3.5546	2.314	0.066	-0.231	-0.0756	-0.4105	-1.6898	-0.358	-0.1633	0.4055	1.2823	1.187	0.0923	-0.294	2.563	0.9561	1.7161
3		2.2754	-0.5929	1.5646	2.2805	-0.825	3.1258	-0.2279	-0.3119	0.1684	0.3896	0.229	-0.1636	-0.0806	-0.1592	-0.0141	0.7277	-0.0201	0.071	0.6933	-0.061	0.6765
4		1.3934	-0.0247	-0.1698	2.9332	0.8517	0.8189	0.0241	-0.1346	-0.2583	-0.397	0.2292	0.1639	-0.0641	0.012	-0.1256	0.8098	0.0588	-0.0532	0.7602	0.0146	0.6641
5		4.4966	3.9316	-1.2889	8.8252	-6.2199	3.783	0.4457	0.0507	-0.374	-0.4332	-1.4091	-2.2821	-0.3106	-0.6186	0.7832	1.7358	0.1505	0.3229	0.6615	-0.201	1.1475
6		0.9286	-0.159	-0.9054	1.563	-0.114	0.4195	-0.1784	-0.7909	0.025	0.701	0.1946	0.4137	-0.0022	-0.8321	0.0019	0.8543	0.069	0.0783	0.9845	-0.0709	0.7084
7		3.2082	2.0852	0.7226	2.1109	0.7603	1.0248	-0.1407	-0.239	-0.3401	-0.0421	0.0427	-0.3946	0.1977	-0.0062	0.0893	0.718	-0.0079	0.0651	0.7077	-0.0407	0.8286
8		2.8508	-3.7244	-0.573	6.1026	0.5542	5.5766	-1.2351	0.7155	0.1886	1.3249	-1.1324	-0.1764	-0.8541	1.2661	2.1964	1.4048	0.1577	-0.2303	1.762	0.278	0.99
9		2.9988	0.6039	-1.0385	1.7266	-1.0086	2.3332	-0.2543	0.4159	-0.066	-0.4633	0.2314	-0.1279	0.3135	-0.2829	0.0525	0.7484	-0.0413	-0.0064	0.7469	-0.0398	0.7128
10		4.0524	2.1514	0.7121	0.7278	-0.2061	3.6233	1.1013	-0.0543	1.0269	0.5944	-0.6496	2.2201	0.8087	0.0474	-0.3644	1.5578	-0.0431	0.1461	0.8546	-0.0884	1.5792
11		2.0232	-0.2286	0.8884	2.3248	0.8628	0.8539	-0.4562	0.1707	0.1721	0.4572	0.3867	0.0636	0.1156	0.0214	0.1525	0.9011	-0.0479	0.032	0.808	0.0366	0.7972
12		0.4812	0.4843	-0.3014	1.0589	-0.5923	1.1703	-0.0855	0.6499	-0.1643	-0.379	0.0953	0.2402	-0.0313	-0.6045	-0.032	0.8548	-0.1061	-0.071	0.9999	-0.0286	0.8184
13		2.6973	-2.632	0.5459	1.5447	-0.0164	1.7347	-0.2439	0.0671	-0.1223	0.2193	0.0416	0.54	0.4367	0.104	0.2122	0.7588	0.0179	0.0919	0.7362	0.0989	0.8644
14		0.6108	-0.0437	-0.4516	1.3898	-0.0696	2.041	0.1947	-0.6058	-0.016	0.6796	0.3225	-0.0118	-0.5585	0.5796	-0.3679	0.8617	0.02	0.0885	0.9156	-0.1646	0.7076
15		3.5688	-0.7044	-1.3966	1.3326	-0.3585	1.3245	-0.3233	-0.4693	-0.6134	0.2352	0.2573	0.2576	0.375	0.0305	0.0485	1.0303	0.116	0.027	0.8981	0.2135	0.8402
16		1.3129	0.0706	-0.9373	1.1028	-0.5918	2.1613	0.1689	0.0394	-0.6735	-0.4902	-0.4656	-1.2063	-0.2068	-0.1877	0.2783	1.5587	0.1122	0.3916	1.3827	-0.0445	2.1677
17		3.4186	-0.678	0.7956	2.4772	0.0686	-0.0964	-0.3611	-0.2501	0.3759	-0.6019	0.4255	-0.1703	0.087	-0.1297	-0.0161	0.9212	0.0343	0.0649	0.7961	0.0685	0.6041
18		1.619	-0.7457	0.8708	1.8375	0.9792	-1.328	-0.079	-0.8448	-0.0174	0.6222	0.2861	-0.4407	0.0952	0.5565	-0.1383	0.9135	0.1907	-0.1662	1.3649	0.0685	0.7027
19		3.2597	1.8245	-0.6482	1.0243	-0.5912	0.8662	-0.2285	-0.1854	0.2363	-0.0332	0.0751	0.3006	-0.3189	0.0644	0.157	0.7122	-0.0289	-0.1313	0.6408	-0.0053	0.8936
20		1.3032	0.4539	0.7992	1.4702	0.1897	1.6734	-0.3193	0.2856	0.2823	-0.371	0.1368	-0.0035	0.4158	0.4754	0.036	0.8827	0.0119	-0.0834	0.9525	-0.1019	0.8693
21		4.6989	-0.2763	1.0739	0.5268	0.0807	2.2933	-0.6998	0.1654	0.9444	0.1823	0.1301	0.1597	-0.2123	-0.1298	0.5626	0.9187	-0.1046	-0.176	0.8261	0.018	1.0184
22		0.4505	-0.7493	-1.575	-0.6363	-0.52	0.0889	0.8946	0.0717	0.2222	-0.5371	-0.5096	0.6479	-0.7535	0.4491	-0.4482	2.2045	-0.1052	-0.1441	0.9702	0.3869	1.2931
23		2.4721	0.3001	1.6523	1.9875	-0.202	0.5346	-0.4717	0.826	-0.1964	-0.2467	0.2423	-0.4	-0.1745	0.2092	0.1846	0.8358	-0.1938	0.1054	1.0229	0.022	0.8402
24		4.9614	2.8883	-0.3169	3.5078	-0.2094	-0.7257	0.2669	1.2459	-0.0689	0.5661	0.259	0.175	-0.4338	-0.3092	-0.6404	0.6643	0.0624	-0.3103	0.8458	0.3081	0.807

Refinement TLS group

Selection details: chain D and resid 712:724)

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