PDB-3p9u: Crystal structure of TetX2 from Bacteroides thetaiotaomicron with...

ID or keywords:

Entry

Database: PDB / ID: 3p9u

Title

Crystal structure of TetX2 from Bacteroides thetaiotaomicron with substrate analogue

Components

TetX2 protein

Keywords

OXIDOREDUCTASE / monooxygenase / tetracycline degradation

Function / homology

Function and homology information

tetracycline 11a-monooxygenase / FAD binding / monooxygenase activity / response to antibiotic / cytoplasm
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.81 Å

Authors

Walkiewicz, K. / Davlieva, M. / Sun, C. / Lau, K. / Shamoo, Y.

Citation

Journal: Proteins / Year: 2011
Title: Crystal structure of Bacteroides thetaiotaomicron TetX2: a tetracycline degrading monooxygenase at 2.8 A resolution.
Authors: Walkiewicz, K. / Davlieva, M. / Wu, G. / Shamoo, Y.

History

Deposition	Oct 18, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jun 19, 2013	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.4	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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	3p9u.cif.gz	305 KB	Display	PDBx/mmCIF format
PDB format	pdb3p9u.ent.gz	247.6 KB	Display	PDB format
PDBx/mmJSON format	3p9u.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p9/3p9u ftp://data.pdbj.org/pub/pdb/validation_reports/p9/3p9u	HTTPS FTP

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Related structure data

Similar structure data	3v3o-1 4a99-2 2xdo-2 2y6r-2 2xdo-1 3v3n-1 3v3n-4 2xyo-4 3v3o-3 2xyo-2 4a99-3 3v3o-4 4guv-2 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TetX2 protein

B: TetX2 protein

C: TetX2 protein

D: TetX2 protein

hetero molecules

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

1

A: TetX2 protein

hetero molecules

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

2

B: TetX2 protein

hetero molecules

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

3

C: TetX2 protein

hetero molecules

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

4

D: TetX2 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	87.700, 67.330, 153.790
Angle α, β, γ (deg.)	90.00, 100.31, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain A and (resseq 3:236 or resseq 241:367 )	A	3 - 236
1	2	1	chain A and (resseq 3:236 or resseq 241:367 )	A	241 - 367
2	1	1	chain B and (resseq 3:236 or resseq 241:367 )	B	3 - 236
2	2	1	chain B and (resseq 3:236 or resseq 241:367 )	B	241 - 367
3	1	1	chain C and (resseq 3:236 or resseq 241:367 )	C	3 - 236
3	2	1	chain C and (resseq 3:236 or resseq 241:367 )	C	241 - 367
4	1	1	chain D and (resseq 3:236 or resseq 241:367 )	D	3 - 236
4	2	1	chain D and (resseq 3:236 or resseq 241:367 )	D	241 - 367

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.913767, -0.067569, -0.40058), (-0.06514, -0.997682, 0.019696), (-0.400982, 0.008096, -0.91605)	85.5765, -39.972301, 63.5065
2	given	(-0.912687, -0.078948, 0.400961), (0.07824, -0.996769, -0.018166), (0.4011, 0.014791, 0.915915)	84.790497, -12.3846, -18.173201
3	given	(-0.999871, 0.015509, -0.004199), (0.01548, 0.999855, 0.007031), (0.004307, 0.006965, -0.999966)	31.0833, 28.435301, 75.935204

#1: Protein	TetX2 protein Mass: 43048.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: tetX2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93L51
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.59 %
Crystal grow	Temperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.6 Details: 2.3M Ammonium Sulfate, 0.1M potassium formate, 0.1M Ches, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 4.2.2 / Wavelength: 0.97889 Å

Detector

Type: NOIR-1 / Detector: CCD / Date: Jun 2, 2010

Radiation

Monochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97889 Å / Relative weight: 1

Reflection

Redundancy: 3.3 % / Av σ(I) over netI: 17.01 / Number: 131098 / R_merge(I) obs: 0.118 / Χ²: 3.06 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 39866 / % possible obs: 92

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
7.59	50	99.7	1	0.059	5.392	3.6
6.03	7.59	100	1	0.088	4.065	3.8
5.27	6.03	100	1	0.093	3.33	3.8
4.79	5.27	99.8	1	0.096	3.415	3.7
4.44	4.79	99.4	1	0.095	3.546	3.7
4.18	4.44	99.4	1	0.097	3.347	3.6
3.97	4.18	99.7	1	0.104	3.155	3.5
3.8	3.97	89.1	1	0.165	8.051	2.5
3.65	3.8	95.6	1	0.149	4.03	3
3.53	3.65	91.4	1	0.186	4.697	2.8
3.42	3.53	87.9	1	0.209	5.396	2.8
3.32	3.42	86.2	1	0.193	2.845	2.9
3.23	3.32	87.4	1	0.16	1.511	3.2
3.15	3.23	85.9	1	0.167	1.356	3.2
3.08	3.15	86.2	1	0.183	1.286	3.2
3.02	3.08	86	1	0.196	1.209	3.2
2.96	3.02	85.6	1	0.213	1.122	3.2
2.9	2.96	87.5	1	0.236	1.012	3.2
2.85	2.9	86	1	0.253	1.003	3.2
2.8	2.85	86.7	1	0.286	0.999	3.2

Reflection

Resolution: 2.8→50 Å / Num. all: 43337 / Num. obs: 39866 / % possible obs: 92 % / Observed criterion σ(F): 1.64 / Redundancy: 3.3 % / R_merge(I) obs: 0.118 / Χ²: 3.061 / Net I/σ(I): 9.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.8-2.85	3.2	0.286	1810	0.999	1	86.7
2.85-2.9	3.2	0.253	1880	1.003	1	86
2.9-2.96	3.2	0.236	1870	1.012	1	87.5
2.96-3.02	3.2	0.213	1842	1.122	1	85.6
3.02-3.08	3.2	0.196	1840	1.209	1	86
3.08-3.15	3.2	0.183	1855	1.286	1	86.2
3.15-3.23	3.2	0.167	1878	1.356	1	85.9
3.23-3.32	3.2	0.16	1863	1.511	1	87.4
3.32-3.42	2.9	0.193	1843	2.845	1	86.2
3.42-3.53	2.8	0.209	1911	5.396	1	87.9
3.53-3.65	2.8	0.186	1973	4.697	1	91.4
3.65-3.8	3	0.149	2070	4.03	1	95.6
3.8-3.97	2.5	0.165	1928	8.051	1	89.1
3.97-4.18	3.5	0.104	2146	3.155	1	99.7
4.18-4.44	3.6	0.097	2153	3.347	1	99.4
4.44-4.79	3.7	0.095	2180	3.546	1	99.4
4.79-5.27	3.7	0.096	2158	3.415	1	99.8
5.27-6.03	3.8	0.093	2185	3.33	1	100
6.03-7.59	3.8	0.088	2213	4.065	1	100
7.59-50	3.6	0.059	2268	5.392	1	99.7

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 2.81 Å / D res low: 48.45 Å / FOM : 0.462 / FOM acentric: 0.499 / FOM centric: 0.355 / Reflection: 38381 / Reflection acentric: 29645 / Reflection centric: 1932

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
9.75-11.18	0.579	0.631	0.272	363	313	47
8.76-9.75	0.579	0.614	0.38	413	358	51
8.01-8.76	0.561	0.59	0.385	447	393	48
7.43-8.01	0.564	0.601	0.342	477	420	48
6.96-7.43	0.584	0.616	0.38	517	456	54
6.57-6.96	0.55	0.579	0.407	547	485	47
6.24-6.57	0.585	0.624	0.338	565	501	45
5.96-6.24	0.557	0.588	0.383	599	532	44
5.71-5.96	0.587	0.607	0.476	626	560	46
5.49-5.71	0.574	0.604	0.341	644	570	35
5.29-5.49	0.564	0.589	0.33	675	591	51
5.11-5.29	0.539	0.553	0.328	705	622	54
4.95-5.11	0.555	0.567	0.417	722	627	44
4.8-4.95	0.533	0.552	0.325	725	643	47
4.67-4.8	0.539	0.55	0.371	794	710	44
4.55-4.67	0.489	0.505	0.259	773	672	51
4.43-4.55	0.51	0.514	0.404	794	692	44
4.33-4.43	0.491	0.505	0.297	842	744	51
4.23-4.33	0.476	0.487	0.305	806	722	45
4.14-4.23	0.471	0.493	0.273	895	783	47
4.05-4.14	0.463	0.48	0.315	874	777	47
3.97-4.05	0.448	0.473	0.356	853	729	38
3.89-3.97	0.375	0.413	0.262	736	426	29
3.82-3.89	0.337	0.369	0.211	741	412	30
3.75-3.82	0.431	0.455	0.363	902	708	44
3.69-3.75	0.415	0.479	0.264	869	587	27
3.62-3.69	0.322	0.342	0.207	844	480	28
3.57-3.62	0.42	0.46	0.27	838	613	29
3.51-3.57	0.438	0.467	0.346	934	703	32
3.46-3.51	0.423	0.465	0.527	792	502	26
3.41-3.46	0.309	0.326	0.213	847	442	25
3.36-3.41	0.411	0.465	0.319	825	569	25
3.31-3.36	0.413	0.433	0.388	938	710	30
3.26-3.31	0.419	0.454	0.3	923	713	33
3.22-3.26	0.424	0.45	0.411	923	708	32
3.18-3.22	0.413	0.447	0.323	993	720	39
3.14-3.18	0.411	0.441	0.401	945	730	27
3.1-3.14	0.428	0.456	0.44	977	713	38
3.07-3.1	0.43	0.469	0.421	975	701	30
3.03-3.07	0.433	0.462	0.455	989	717	27
3-3.03	0.431	0.463	0.29	1002	737	37
2.96-3	0.44	0.482	0.401	991	711	29
2.93-2.96	0.445	0.477	0.385	1005	721	37
2.9-2.93	0.449	0.483	0.434	1047	745	32
2.87-2.9	0.437	0.478	0.489	1027	735	27
2.84-2.87	0.449	0.483	0.365	1012	703	34
2.81-2.84	0.463	0.51	0.39	949	683	25

Phasing dm

FOM : 0.66 / FOM acentric: 0.66 / FOM centric: 0.56 / Reflection: 38452 / Reflection acentric: 36519 / Reflection centric: 1933

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5-8	0.73	0.75	0.57	5777	5325	452
4-5	0.75	0.76	0.6	7174	6764	410
3.5-4	0.71	0.71	0.59	6343	6104	239
3-3.5	0.59	0.59	0.54	10729	10376	353
2.8-3	0.51	0.51	0.46	6512	6311	201

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
RESOLVE	2.15	phasing
PHENIX	1.6.4_486	refinement
PDB_EXTRACT	3.1	data extraction
JBluIce-EPICS		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.81→48.45 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7202 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2817	1990	5.19 %	RANDOM
R_work	0.2383	-	-	-
obs	0.2405	38376	88.34 %	-
all	-	43337	-	-

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 18.032 Å² / k_sol: 0.348 e/Å³

Displacement parameters

B_iso max: 103.73 Å² / B_iso mean: 25.1826 Å² / B_iso min: 0.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.631 Å²	0 Å²	0.8052 Å²
2-	-	-0.4908 Å²	0 Å²
3-	-	-	2.1218 Å²

Refinement step

Cycle: LAST / Resolution: 2.81→48.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11587	0	232	90	11909

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	12091
X-RAY DIFFRACTION	f_angle_d	1.247	16369
X-RAY DIFFRACTION	f_chiral_restr	0.096	1768
X-RAY DIFFRACTION	f_plane_restr	0.005	2122
X-RAY DIFFRACTION	f_dihedral_angle_d	19.286	4649

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	2841	X-RAY DIFFRACTION	POSITIONAL	0.054
1	2	B	2841	X-RAY DIFFRACTION	POSITIONAL	0.054
1	3	C	2841	X-RAY DIFFRACTION	POSITIONAL	0.057
1	4	D	2848	X-RAY DIFFRACTION	POSITIONAL	0.049

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.8103-2.8805	0.3633	126	0.2946	2289	2415	79
2.8805-2.9584	0.3985	130	0.2872	2383	2513	82
2.9584-3.0454	0.3212	132	0.2813	2425	2557	83
3.0454-3.1437	0.3218	134	0.2674	2442	2576	83
3.1437-3.2561	0.311	135	0.2675	2462	2597	84
3.2561-3.3864	0.3262	135	0.2691	2449	2584	84
3.3864-3.5405	0.3554	128	0.3136	2328	2456	79
3.5405-3.7271	0.3342	136	0.2818	2514	2650	86
3.7271-3.9605	0.2911	137	0.2478	2496	2633	85
3.9605-4.2661	0.2285	157	0.1948	2849	3006	98
4.2661-4.6951	0.2105	160	0.1735	2920	3080	99
4.6951-5.3737	0.2315	158	0.195	2909	3067	99
5.3737-6.7674	0.2395	162	0.2173	2949	3111	98
6.7674-48.457	0.2332	160	0.2037	2971	3131	97

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