PDB-3nib: Teg14 Apo

ID or keywords:

Entry

Database: PDB / ID: 3nib

Title

Teg14 Apo

Components

Teg14

Keywords

TRANSFERASE / Antibiotic Transferase

Function / homology

Sulfotransferase domain / Sulfotransferase domain / sulfotransferase activity / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / Teg14

Function and homology information

Biological species

uncultured soil bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Bick, M.J. / Banik, J.J. / Darst, S.A. / Brady, S.F.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: The 2.7 A resolution structure of the glycopeptide sulfotransferase Teg14
Authors: Bick, M.J. / Banik, J.J. / Darst, S.A. / Brady, S.F.

History

Deposition	Jun 15, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 8, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Mar 28, 2012	Group: Database references
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ni/3nib ftp://data.pdbj.org/pub/pdb/validation_reports/ni/3nib	HTTPS FTP

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Related structure data

Related structure data	3mgbS S: Starting model for refinement
Similar structure data	2ovf-1 1p91-d 2pif-d 5apk-d 5g5k-d 2ov8-1 5qsz-2 2zne-d 4dpu-d 3com-d 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	#116 - Aug 2009 Sulfotransferases similarity (2)

Deposited unit

A: Teg14

hetero molecules

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

1

A: Teg14

hetero molecules

A: Teg14

hetero molecules

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

Unit cell

Length a, b, c (Å)	112.194, 112.194, 74.807
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Teg14 Mass: 34477.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured soil bacterium (environmental samples) Gene: teg14 / Plasmid: pET28a (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: B7T1D9, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Chemical	ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₇NO₃S / Comment: pH buffer*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.94 Å³/Da / Density % sol: 68.8 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: Crystallized at 20mg/ml using JCSG solution core II number 3 (1.0 M sodium citrate, 0.1 M CHES, pH 9.5) as the precipitant. Drop was a 1:1 mixture of protein and crystallization solution. ...Details: Crystallized at 20mg/ml using JCSG solution core II number 3 (1.0 M sodium citrate, 0.1 M CHES, pH 9.5) as the precipitant. Drop was a 1:1 mixture of protein and crystallization solution. Reservoir volume was 500 ul. Crystals appeared overnight, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

Crystal

Density Matthews: 3.94 Å³/Da / Density % sol: 68.8 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: Crystallized at 20mg/ml using JCSG solution core II number 3 (1.0 M sodium citrate, 0.1 M CHES, pH 9.5) as the precipitant. Drop was a 1:1 mixture of protein and crystallization solution. ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 30, 2008 / Details: Varimax confocal Max-Flux optics
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.7→25 Å / Num. all: 14590 / Num. obs: 13977 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / R_merge(I) obs: 0.073 / R_sym value: 0.073 / Net I/σ(I): 14.6
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.494 / Mean I/σ(I) obs: 2.49 / Num. unique all: 1382 / R_sym value: 0.494 / % possible all: 93.1

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Processing

Software

Name	Version	Classification
CrystalClear		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.5_2)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Teg12 ternary, pdb code 3MGB

3mgb

Resolution: 2.7→22.786 Å / SU ML: 0.33 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2356	678	4.97 %	Random
R_work	0.1955	-	-	-
obs	0.1975	13643	89.76 %	-
all	-	14585	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 79.853 Å² / k_sol: 0.365 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.4918 Å²	0 Å²	-0 Å²
2-	-	4.4918 Å²	0 Å²
3-	-	-	-8.9835 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→22.786 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1797	0	25	54	1876

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	1859
X-RAY DIFFRACTION	f_angle_d	0.805	2521
X-RAY DIFFRACTION	f_dihedral_angle_d	14.59	654
X-RAY DIFFRACTION	f_chiral_restr	0.052	285
X-RAY DIFFRACTION	f_plane_restr	0.004	321

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 (%)
2.7004-2.9085	0.3508	123	0.282	2222	X-RAY DIFFRACTION	79
2.9085-3.2005	0.303	117	0.2227	2326	X-RAY DIFFRACTION	81
3.2005-3.6619	0.2103	149	0.1809	2661	X-RAY DIFFRACTION	93
3.6619-4.6074	0.2142	150	0.1582	2825	X-RAY DIFFRACTION	98
4.6074-22.7867	0.213	139	0.1976	2931	X-RAY DIFFRACTION	97

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	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	1.1224	-0.0979	0.4967	0.4728	-0.7904	1.3974	-0.1365	0.1187	0.465	0.0879	0.1037	0.0129	-0.0019	-0.1867	-0.0001	0.2732	-0.0728	0.0064	0.279	-0.0004	0.3194	38.6554	-31.0358	-25.7622
2	0.4298	0.1307	0.4815	0.2447	0.1186	0.6956	0.0723	0.7348	-0.4821	-0.0243	0.4518	-0.4553	-0.1068	0.9596	0.022	0.5049	-0.0543	-0.0059	0.3202	0.0022	0.3311	54.4154	-35.3535	-28.4113
3	0.2651	0.0725	0.3132	0.4315	-0.2051	0.5573	-0.1055	0.4843	1.1102	0.1199	-0.075	-0.3486	-0.654	-0.0688	0.0006	0.3457	-0.0483	-0.0113	0.2566	0.0483	0.3288	48.6383	-26.1737	-21.4024
4	0.2604	0.0355	0.1606	0.4247	-0.4786	0.677	-0.1612	-0.1816	0.3465	0.1178	-0.1461	0.8226	-0.1719	0.1568	0.0006	0.2318	-0.0651	-0.0235	0.3755	0.001	0.3244	52.8211	-30.5503	-13.5689
5	2.8571	-1.1508	1.0174	0.6404	-0.5056	0.417	0.7925	0.4486	-2.5544	0.7609	0.7005	2.0169	1.7553	-0.5942	0.0368	0.6947	-0.1584	-0.0426	0.4505	0.0114	0.7509	50.6857	-47.9858	-15.4404
6	0.1181	0.144	-0.152	0.1659	-0.1793	0.1896	-0.1651	-0.7365	-0.8098	0.6666	0.5417	0.7587	-0.1613	-1.0264	-0.0021	0.5111	-0.0362	0.0467	0.5812	0.1726	0.4826	40.4987	-40.7667	-12.6568
7	0.4145	0.3252	0.1124	0.2551	0.1244	0.3192	-0.2305	-0.3866	0.3903	-0.6093	0.4909	-0.4726	0.1523	0.5242	0.001	0.2774	-0.1737	0.0403	0.459	-0.035	0.4135	27.2437	-39.5568	-20.4042
8	0.0444	-0.0391	-0.0256	0.1561	-0.0874	0.0917	-0.2469	1.15	0.5555	-0.0979	-0.3428	0.1465	0.0406	-0.8382	-0.0006	0.2553	-0.1059	-0.0456	0.5557	-0.0057	0.4074	27.3987	-31.9227	-29.7818
9	0.4631	-0.0505	-0.0271	0.0149	-0.0061	0.0114	-0.9747	-0.8676	-0.8394	1.0062	-0.4247	-2.0863	0.1232	0.4133	0.0001	0.7309	-0.0729	0.2091	0.3472	0.1928	0.6312	48.6268	-48.1953	-34.3775
10	4.3579	-2.8105	-1.7513	3.0015	1.324	1.7938	-0.8204	0.2215	-1.4153	-0.1649	0.5171	0.4698	1.8901	-0.2892	-0.0737	0.9107	-0.1995	0.2379	0.2738	-0.233	0.7684	42.5001	-53.9483	-39.9293
11	1.2294	-0.0208	-0.2866	1.0716	0.4765	1.1216	0.1124	0.9264	0.0359	-0.8635	-0.2962	0.0932	-0.3287	-1.2354	-0.0134	0.388	-0.0674	-0.0928	0.5309	0.0458	0.3526	35.5298	-33.684	-36.7007
12	0.0769	0.0364	-0.0406	0.0402	-0.0317	0.0273	0.6104	-0.3628	-0.145	-0.4927	-0.1828	0.0347	0.3954	0.9898	0.0043	0.9493	0.0556	0.2763	0.4237	-0.1377	0.8996	54.5776	-55.0434	-40.2967
13	0.3738	0.2075	-0.2651	0.1305	-0.1309	0.1902	-0.3732	0.7675	-0.0482	-0.5748	-0.0817	0.1043	0.043	-1.0929	-0.0001	0.6285	-0.2308	0.2821	0.4706	-0.1713	0.4844	50.353	-48.1628	-47.2467
14	0.554	0.1064	-0.3192	0.263	-0.137	0.2033	-0.7898	1.2986	0.3419	0.1948	0.3281	0.4569	0.2231	-1.136	-0.0003	0.4923	-0.1942	0.0132	0.4803	-0.0727	0.3015	47.2975	-36.4494	-43.7925
15	0.7499	0.4922	0.2602	1.2437	0.7471	1.8386	0.2166	-0.4624	-0.2425	0.6823	-0.0992	0.2721	0.7963	-0.2223	0.0028	0.1596	0.0184	-0.012	0.2906	0.0124	0.277	45.9061	-35.9029	-16.4765

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and (resid 0:12) or chain A and (resid 57:67) or chain A and (resid 83:90) or chain A and (resid 157:165)
2	X-RAY DIFFRACTION	2	chain A and (resid 166:170)
3	X-RAY DIFFRACTION	3	chain A and (resid 171:186)
4	X-RAY DIFFRACTION	4	chain A and (resid 187:203)
5	X-RAY DIFFRACTION	5	chain A and (resid 204:211)
6	X-RAY DIFFRACTION	6	chain A and (resid 31:42)
7	X-RAY DIFFRACTION	7	chain A and (resid 43:56)
8	X-RAY DIFFRACTION	8	chain A and (resid 68:82)
9	X-RAY DIFFRACTION	9	chain A and (resid 91:101)
10	X-RAY DIFFRACTION	10	chain A and (resid 109:127)
11	X-RAY DIFFRACTION	11	chain A and (resid 133:156)
12	X-RAY DIFFRACTION	12	chain A and (resid 241:248)
13	X-RAY DIFFRACTION	13	chain A and (resid 249:261)
14	X-RAY DIFFRACTION	14	chain A and (resid 262:275)
15	X-RAY DIFFRACTION	15	chain A and (resid 13:30)

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