PDB-4dq0: The crystal structure of tellurite resistance protein from Escher...

ID or keywords:

Entry

Database: PDB / ID: 4dq0

Title

The crystal structure of tellurite resistance protein from Escherichia coli O157:H7 str. Sakai

Components

Tellurite resistance protein

Keywords

TRANSFERASE / structural genomics / PSI-Biology / Protein Structure Initiative / MCSG / Midwest Center for Structural Genomics

Function / homology

Function and homology information

response to tellurium ion / S-adenosylmethionine-dependent methyltransferase activity / methylation / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.199 Å

Authors

Tan, K. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of tellurite resistance protein from Escherichia coli O157:H7 str. Sakai
Authors: Tan, K. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A.

History

Deposition	Feb 14, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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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Download

PDBx/mmCIF format	4dq0.cif.gz	329.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4dq0.ent.gz	270.9 KB	Display	PDB format
PDBx/mmJSON format	4dq0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4dq0_validation.pdf.gz	464.8 KB	Display	wwPDB validaton report
Full document	4dq0_full_validation.pdf.gz	474.1 KB	Display
Data in XML	4dq0_validation.xml.gz	33.3 KB	Display
Data in CIF	4dq0_validation.cif.gz	46.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dq/4dq0 ftp://data.pdbj.org/pub/pdb/validation_reports/dq/4dq0	HTTPS FTP

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Related structure data

Related structure data	2xvmS S: Starting model for refinement
Similar structure data	3zs3-d 4hyf-2 6l79-d 4hyf-3 4jvw-1 4i9i-3 6m1s-2 4li7-2 4ksh-d 5fgt-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) 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
Other databases	TargetTrack: MCSG-APC102457

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tellurite resistance protein

B: Tellurite resistance protein

C: Tellurite resistance protein

D: Tellurite resistance protein

hetero molecules

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

1

A: Tellurite resistance protein

hetero molecules

defined by author&software
22.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tellurite resistance protein

hetero molecules

defined by author&software
23.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Tellurite resistance protein

hetero molecules

defined by author&software
23.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Tellurite resistance protein

defined by author&software
22.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	174.870, 61.034, 77.145
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Details

Experimentally unknown. The protein is predicted to be monomeric.

#1: Protein	Tellurite resistance protein Mass: 22707.844 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 str. Sakai / Gene: ECs2035, Escherichia coli, tehB, Z2288 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q8X9V6
#2: Chemical	ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES Mass: 207.290 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₇NO₃S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.27 Å³/Da / Density % sol: 45.72 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.1M CHES:NaOH, 30% (w/v) PEG3000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2012 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97931 Å / Relative weight: 1
Reflection	Resolution: 2.2→37 Å / Num. all: 42669 / Num. obs: 42669 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / R_merge(I) obs: 0.134 / Net I/σ(I): 14.8
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.678 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2075 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 2XVM

2xvm

Resolution: 2.199→36.992 Å / SU ML: 0.61 / σ(F): 1.34 / Phase error: 25.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2462	2144	5.03 %	random
R_work	0.1791	-	-	-
obs	0.1825	42628	99.49 %	-
all	-	42628	-	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 18.067 Å² / k_sol: 0.289 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.3046 Å²	0 Å²	-0 Å²
2-	-	5.0376 Å²	0 Å²
3-	-	-	-6.3421 Å²

Refinement step

Cycle: LAST / Resolution: 2.199→36.992 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6256	0	65	329	6650

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6441
X-RAY DIFFRACTION	f_angle_d	1.057	8699
X-RAY DIFFRACTION	f_dihedral_angle_d	14.253	2395
X-RAY DIFFRACTION	f_chiral_restr	0.072	957
X-RAY DIFFRACTION	f_plane_restr	0.004	1114

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 (%)
2.199-2.2502	0.333	147	0.2273	2498	X-RAY DIFFRACTION	94
2.2502-2.3065	0.3221	141	0.2295	2654	X-RAY DIFFRACTION	100
2.3065-2.3688	0.3241	150	0.219	2678	X-RAY DIFFRACTION	100
2.3688-2.4385	0.3028	133	0.2119	2690	X-RAY DIFFRACTION	100
2.4385-2.5172	0.2835	130	0.1984	2668	X-RAY DIFFRACTION	100
2.5172-2.6071	0.2885	139	0.1926	2666	X-RAY DIFFRACTION	100
2.6071-2.7115	0.2638	159	0.1982	2667	X-RAY DIFFRACTION	100
2.7115-2.8349	0.3439	141	0.21	2707	X-RAY DIFFRACTION	100
2.8349-2.9843	0.3081	135	0.2116	2700	X-RAY DIFFRACTION	100
2.9843-3.1711	0.2717	138	0.201	2706	X-RAY DIFFRACTION	100
3.1711-3.4158	0.2534	137	0.1955	2726	X-RAY DIFFRACTION	100
3.4158-3.7593	0.2274	151	0.1676	2702	X-RAY DIFFRACTION	100
3.7593-4.3025	0.1967	151	0.1447	2743	X-RAY DIFFRACTION	100
4.3025-5.418	0.1686	156	0.1274	2763	X-RAY DIFFRACTION	100
5.418-36.9969	0.2141	136	0.1669	2916	X-RAY DIFFRACTION	99

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	5.5127	-0.6834	1.8876	4.7357	0.3637	4.6966	-0.3181	-1.2201	0.299	0.7176	0.0503	0.6923	-0.3367	-0.8892	-0.1246	0.5188	0.0938	0.0835	0.6469	-0.0422	0.2465	11.4639	20.5291	24.4769
2	4.2878	0.0422	0.7333	3.468	0.5408	3.8902	0.0275	-0.5123	-0.0041	0.4121	0.0086	0.1483	-0.1581	-0.339	-0.0681	0.2158	0.0095	0.0202	0.1943	0.0665	0.1962	9.7397	18.6064	12.8618
3	1.7655	-0.2975	0.1502	1.3404	0.3737	3.0996	0.0093	-0.3321	-0.4223	0.197	0.0494	-0.0174	0.5156	0.2135	-0.0786	0.2643	0.0451	-0.0427	0.2024	0.0849	0.2494	19.6636	11.6623	11.0658
4	1.1417	-0.3055	0.1688	2.3758	-0.4931	1.1077	0.0344	0.0567	-0.0145	0.1262	-0.0819	-0.104	-0.0317	0.1041	0.0354	0.1269	0.0075	-0.013	0.0699	0.0077	0.1388	13.8102	22.516	-2.0628
5	2.9941	0.2453	1.5811	2.8499	0.1616	2.2597	-0.0766	0.1602	0.0266	-0.1206	0.052	-0.0423	-0.2216	-0.0728	0.065	0.1775	0.0287	0.022	0.1688	0.002	0.1629	12.8117	27.8696	-7.3724
6	3.0648	-0.4545	0.1739	2.4523	-0.5298	2.7204	-0.0328	-0.3196	0.3727	0.4332	0.0821	-0.0725	-0.4089	0.2626	0.1494	0.2188	-0.0205	0.0237	0.2262	-0.0555	0.2294	8.4452	32.1596	3.5636
7	2.0863	-0.7777	-0.0967	3.663	-0.4875	3.0844	0.1011	-0.1677	0.1679	0.332	-0.1893	0.3209	0.0272	0.003	0.0957	0.0517	0.0145	0.0335	0.1009	-0.0132	0.1329	6.4807	26.5891	-0.301
8	0.8366	-0.032	0.6673	5.8664	-2.2917	2.836	-0.0041	-0.2378	0.3411	0.594	0.0091	0.1073	-0.4229	-0.1899	-0.0852	0.2015	0.0215	0.0311	0.1599	-0.001	0.3029	19.7975	56.6263	1.6165
9	3.8215	-0.2717	0.014	3.338	-1.0097	3.8427	-0.0178	-0.0357	0.247	0.1778	0.0335	0.2972	-0.0261	-0.0513	-0.0032	0.1518	0.0025	0.0069	0.076	-0.0097	0.2001	30.6926	51.9407	1.7918
10	4.3785	1.0746	2.3379	5.835	4.6612	5.2834	0.1131	0.0333	0.0301	-0.0937	-0.0854	-0.0643	-0.1292	0.2605	-0.0481	0.0835	0.004	0.0494	0.1125	0.0254	0.1852	30.0519	48.952	-6.3055
11	3.6788	-0.1771	1.1008	1.4766	0.2632	2.2729	0.0702	0.2754	-0.0817	-0.1875	-0.0715	0.1532	0.0342	0.0853	0.0093	0.179	0.0034	0.027	0.1121	0.0115	0.1177	28.541	47.854	-10.0857
12	1.7777	0.1132	-0.1246	2.5806	-0.2334	1.8625	0.0266	0.0164	-0.0799	-0.0065	-0.0083	0.0803	0.2125	0.067	0.0223	0.1471	0.0462	-0.0147	0.0967	-0.0164	0.146	35.8668	37.5517	3.7442
13	3.0844	1.4121	0.7946	4.3797	1.1792	3.1105	-0.2162	-0.2728	-0.2277	0.2477	0.1699	-0.4499	0.1325	0.3481	0.0632	0.1157	0.03	-0.01	0.1682	0.0094	0.166	40.2431	37.0665	9.6218
14	3.0199	2.1661	3.0082	2.7548	1.2032	3.753	0.1107	-0.7949	-0.1601	0.3569	0.0447	0.5085	-0.119	-0.6804	-0.1368	0.335	0.0533	0.082	0.3839	0.0578	0.362	19.0706	35.5382	15.47
15	2.8905	1.5799	-0.6621	3.7923	-0.8586	2.8882	0.3259	-0.4546	-0.0291	0.451	-0.0658	0.0235	-0.1828	0.1317	-0.1221	0.1076	0.0194	-0.0076	0.0962	0.0052	0.1325	35.9202	41.345	11.4457
16	4.8061	0.8243	-1.6438	3.0581	-0.4777	2.3436	-0.1517	1.1125	-0.7209	-0.6358	0.1242	-0.4448	0.948	0.3481	-0.0239	0.4938	0.0587	0.0188	0.4595	-0.1144	0.2678	26.7641	9.6424	-29.0839
17	2.6792	0.4959	-0.819	1.5586	-0.3315	1.887	-0.0013	0.0065	-0.0176	-0.1716	-0.1887	-0.1515	0.3232	0.6625	0.073	0.17	0.1617	0.0198	0.3331	0.087	0.1188	33.3115	18.6585	-21.0423
18	1.1058	0.0407	-0.2117	1.9695	-0.3536	2.3933	-0.0603	0.3481	0.1802	-0.3339	-0.173	-0.014	-0.2406	0.6921	-0.0956	0.1266	-0.0031	0.0867	0.5398	0.1378	0.1003	35.5529	31.2471	-34.3082
19	0.7524	0.1956	0.6561	1.3239	-0.8474	4.0471	-0.0734	0.1515	-0.0123	-0.2985	-0.0449	0.2346	-0.1272	-0.8364	-0.1571	0.6427	0.0303	-0.0258	0.9115	-0.0477	0.0954	8.1245	42.2853	-51.5448
20	5.041	-0.1647	-1.6115	2.9771	0.1608	3.6983	0.1595	0.6864	-0.4527	-0.1856	-0.1435	-0.0644	0.2973	-0.0063	0.0854	0.3459	0.0296	-0.0508	0.4164	0.0195	0.2249	7.5418	39.2322	-41.8641
21	2.3896	0.5387	-0.3011	2.3088	0.179	1.8964	0.1816	0.6092	0.3382	-0.3331	-0.2763	-0.0158	-0.082	0.0894	0.0484	0.2663	0.0367	-0.0418	0.2732	0.1058	0.2191	7.5228	47.7355	-38.6841
22	1.4715	0.6077	-0.0314	0.9045	-0.2356	3.3074	-0.0893	0.4395	0.5339	-0.1846	-0.0927	-0.1037	-0.6973	0.3093	0.1572	0.3761	-0.0032	0.0113	0.2943	0.1398	0.2988	15.4241	53.073	-37.7291
23	2.5514	-0.2859	0.7679	1.7612	-0.4939	2.5053	-0.0143	0.1289	0.2686	0.1571	-0.1067	-0.0491	-0.2906	0.0667	0.0886	0.1677	-0.0031	0.0052	0.1235	0.0263	0.1696	10.8266	45.5799	-25.3671
24	2.3201	0.0088	0.4241	2.4798	-0.4103	2.0046	-0.0071	-0.1014	0.0016	0.0645	-0.0274	-0.0078	0.0642	-0.1398	0.0285	0.1461	0.0052	0.0074	0.1247	-0.012	0.1024	9.1847	34.456	-21.0447
25	5.6836	1.1024	-4.0774	1.7025	-1.1221	4.9651	-0.4779	0.8794	-0.7078	-0.6012	0.3128	-0.1879	0.2018	0.4457	0.0742	0.3072	-0.0075	-0.0093	0.4735	-0.1549	0.3334	13.5274	25.2522	-33.9454
26	2.2988	0.8975	0.2374	2.298	-1.0339	2.7237	0.1081	0.4216	-0.3374	-0.4547	-0.2133	0.2086	0.3339	0.0348	0.0902	0.1507	0.0008	-0.0289	0.1766	-0.0122	0.1085	7.3786	33.4291	-27.9777

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 3:13)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 14:51)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 52:97)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 98:145)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 146:159)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 160:184)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 185:197)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 0:19)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 20:50)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 51:61)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 62:97)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 98:145)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 146:169)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 170:184)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 185:197)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 0:19)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 20:97)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 98:197)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 2:12)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 13:27)
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 28:51)
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 52:97)
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 98:135)
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 136:169)
25	X-RAY DIFFRACTION	25	chain 'D' and (resseq 170:182)
26	X-RAY DIFFRACTION	26	chain 'D' and (resseq 183:197)

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-Aug 12, 2020. Covid-19 info

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+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi