PDB-6yr2: TetR(D) soaked with Tigecycline P4(1)2(1)2

ID or keywords:

Entry

Database: PDB / ID: 6yr2

Title

TetR(D) soaked with Tigecycline P4(1)2(1)2

Components

Tetracycline repressor protein class D

Keywords

TRANSCRIPTION

Function / homology

Function and homology information

transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / metal ion binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Hinrichs, W. / Stary, K.

Citation

Journal: to be published
Title: TetR(D) soaked with Tigecycline
Authors: Hinrichs, W. / Stary, K.

History

Deposition	Apr 19, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 28, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6yr2.cif.gz	168.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6yr2.ent.gz		Display	PDB format
PDBx/mmJSON format	6yr2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6yr2_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6yr2_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6yr2_validation.xml.gz	19.4 KB	Display
Data in CIF	6yr2_validation.cif.gz	27.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yr/6yr2 ftp://data.pdbj.org/pub/pdb/validation_reports/yr/6yr2	HTTPS FTP

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Related structure data

Related structure data	6yr1C 2xpvS 1ork 4abz C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2fj1-1 6rgx-d 6rbl-1 6rbm-1 2xrl-1 2xb5-1 5fkk-d 2o7o-1 4ac0-1 4aux-1 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

Deposited unit

AAA: Tetracycline repressor protein class D

BBB: Tetracycline repressor protein class D

hetero molecules

47.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: homology, 4ABZ, 6YR1

Unit cell

Length a, b, c (Å)	68.339, 68.339, 178.397
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain: (Details: Chains AAA BBB)

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Protein , 1 types, 2 molecules AAABBB

#1: Protein	Tetracycline repressor protein class D Mass: 23288.334 Da / Num. of mol.: 2 / Mutation: A2S Source method: isolated from a genetically manipulated source Details: RA1 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tetR / Details (production host): pWH1950 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ACT4

#1: Protein

Tetracycline repressor protein class D

Mass: 23288.334 Da / Num. of mol.: 2 / Mutation: A2S
Source method: isolated from a genetically manipulated source
Details: RA1 plasmid / Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: tetR / Details (production host): pWH1950 / Production host:

Escherichia coli K-12 (bacteria) / References: UniProt: P0ACT4

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Non-polymers , 5 types, 177 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-T1C / TIGECYCLINE Mass: 587.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₉H₄₁N₅O₈ / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.24 Å³/Da / Density % sol: 44.99 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Native crystal soaked in 1M (NH4)2SO4, 0.2M NaCl, 0.05M Tris/HCl, pH 7.0, 0.142 mM TigeTC, 2mM MgCl2, 14hours.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU SATURN 70 / Detector: CCD / Date: Nov 11, 2009
Radiation	Monochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.95→42.5 Å / Num. obs: 31779 / % possible obs: 97.9 % / Redundancy: 7.33 % / B_iso Wilson estimate: 29 Å² / R_merge(I) obs: 0.143 / Χ²: 0.73 / Net I/σ(I): 7.1
Reflection shell	Resolution: 1.95→2.02 Å / Redundancy: 4.52 % / R_merge(I) obs: 0.639 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2855 / Χ²: 0.65 / % possible all: 92.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
CrystalClear		data reduction
CrystalClear		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2xpv

2xpv

Resolution: 1.95→37.53 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.932 / SU B: 11.06 / SU ML: 0.137 / Cross valid method: FREE R-VALUE / ESU R: 0.195 / ESU R Free: 0.162
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2374	1569	5.037 %
R_work	0.2102	-	-
all	0.212	-	-
obs	-	31150	98.076 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 34.691 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.435 Å²	-0 Å²	-0 Å²
2-	-	0.435 Å²	0 Å²
3-	-	-	-0.87 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→37.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3196	0	61	165	3422

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	3323
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	3106
X-RAY DIFFRACTION	r_angle_refined_deg	1.964	1.66	4510
X-RAY DIFFRACTION	r_angle_other_deg	1.538	1.587	7161
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.549	5	404
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.966	21.518	191
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.895	15	567
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.416	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	428
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3737
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	707
X-RAY DIFFRACTION	r_nbd_refined	0.23	0.2	803
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	2834
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1685
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.091	0.2	1448
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.184	0.2	155
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.043	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.259	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.205	0.2	107
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.137	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	1.637	1.408	1622
X-RAY DIFFRACTION	r_mcbond_other	1.637	1.408	1621
X-RAY DIFFRACTION	r_mcangle_it	2.715	2.095	2024
X-RAY DIFFRACTION	r_mcangle_other	2.715	2.096	2025
X-RAY DIFFRACTION	r_scbond_it	2.02	1.623	1701
X-RAY DIFFRACTION	r_scbond_other	1.95	1.612	1698
X-RAY DIFFRACTION	r_scangle_it	3.273	2.368	2486
X-RAY DIFFRACTION	r_scangle_other	3.217	2.352	2480
X-RAY DIFFRACTION	r_lrange_it	5.199	16.111	3898
X-RAY DIFFRACTION	r_lrange_other	5.181	16.085	3880
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.147	0.05	5933

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 (%)
1.95-2.001	0.345	91	0.297	2009	X-RAY DIFFRACTION	92.4296
2.001-2.055	0.326	112	0.277	1996	X-RAY DIFFRACTION	93.6473
2.055-2.115	0.29	116	0.25	1945	X-RAY DIFFRACTION	95.1524
2.115-2.18	0.257	97	0.231	1950	X-RAY DIFFRACTION	96.6478
2.18-2.251	0.226	91	0.214	1928	X-RAY DIFFRACTION	97.6778
2.251-2.33	0.251	130	0.216	1840	X-RAY DIFFRACTION	98.7469
2.33-2.418	0.232	107	0.208	1823	X-RAY DIFFRACTION	99.4845
2.418-2.517	0.268	86	0.203	1755	X-RAY DIFFRACTION	99.7291
2.517-2.628	0.263	114	0.217	1698	X-RAY DIFFRACTION	99.9448
2.628-2.756	0.235	78	0.204	1616	X-RAY DIFFRACTION	100
2.756-2.905	0.267	78	0.225	1552	X-RAY DIFFRACTION	100
2.905-3.081	0.324	66	0.234	1515	X-RAY DIFFRACTION	100
3.081-3.293	0.253	73	0.235	1382	X-RAY DIFFRACTION	99.8627
3.293-3.556	0.241	72	0.212	1310	X-RAY DIFFRACTION	100
3.556-3.895	0.201	68	0.189	1194	X-RAY DIFFRACTION	99.8418
3.895-4.352	0.196	67	0.18	1099	X-RAY DIFFRACTION	99.6581
4.352-5.022	0.167	48	0.151	983	X-RAY DIFFRACTION	99.5174
5.022-6.141	0.211	37	0.207	868	X-RAY DIFFRACTION	99.8896
6.141-8.644	0.226	21	0.196	692	X-RAY DIFFRACTION	99.3036
8.644-37.53	0.157	17	0.216	420	X-RAY DIFFRACTION	97.3274

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	2.164	0.1975	2.5105	0.126	-0.016	3.4877	-0.0209	0.0033	0.0048	0.0102	-0.0351	-0.0063	-0.0144	0.0592	0.056	0.2085	0.0361	-0.0353	0.2528	0.0156	0.2495	65.7558	10.9295	31.0282
2	0.6416	-0.1356	-0.2058	0.1282	-0.2479	0.9556	0.0286	-0.042	0.0192	-0.0354	0.0104	-0.0211	0.0445	0.0577	-0.0391	0.2363	-0.0398	0.0145	0.2473	-0.0101	0.2745	58.9785	16.1112	4.5912
3	1.99	0.2393	0.2476	0.206	0.1286	0.1134	-0.1756	-0.1217	-0.2055	0.1507	0.0329	0.1603	0.17	-0.0231	0.1428	0.5627	-0.0636	0.3399	0.0449	0.0182	0.3264	34.3048	4.2327	12.3826
4	1.1009	0.2096	-1.4926	0.1945	0.0115	2.6159	0.0644	-0.1134	-0.0353	-0.0453	-0.0467	-0.0105	-0.1697	0.0582	-0.0177	0.2258	0.0041	0.0302	0.2616	0.0038	0.2745	35.5548	22.4627	30.8129
5	0.4812	-0.13	-0.1524	0.2805	0.2782	1.2205	0.044	0.0325	0.0049	-0.0052	0.0065	0.0482	-0.0278	0.009	-0.0505	0.2368	-0.044	0.0156	0.2239	0.0024	0.2799	41.0054	18.6777	4.6047
6	6.3212	-4.6138	-0.607	3.7971	0.9438	0.6667	0.0841	-0.092	-0.004	0.1876	-0.0069	0.0125	0.2236	-0.057	-0.0772	0.3211	-0.135	0.1697	0.1391	-0.053	0.3851	67.277	33.2546	7.0018

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	2 - 45
2	X-RAY DIFFRACTION	1	ALL	AAA	46 - 63
3	X-RAY DIFFRACTION	2	ALL	AAA	64 - 93
4	X-RAY DIFFRACTION	2	ALL	AAA	101 - 106
5	X-RAY DIFFRACTION	2	ALL	AAA	107 - 123
6	X-RAY DIFFRACTION	2	ALL	AAA	94 - 100
7	X-RAY DIFFRACTION	2	ALL	AAA	124 - 155
8	X-RAY DIFFRACTION	2	ALL	AAA	182 - 208
9	X-RAY DIFFRACTION	3	ALL	AAA	156 - 181
10	X-RAY DIFFRACTION	4	ALL	BBB	2 - 45
11	X-RAY DIFFRACTION	4	ALL	BBB	46 - 63
12	X-RAY DIFFRACTION	5	ALL	BBB	64 - 93
13	X-RAY DIFFRACTION	5	ALL	BBB	101 - 106
14	X-RAY DIFFRACTION	5	ALL	BBB	107 - 123
15	X-RAY DIFFRACTION	5	ALL	BBB	94 - 100
16	X-RAY DIFFRACTION	5	ALL	BBB	124 - 156
17	X-RAY DIFFRACTION	5	ALL	BBB	182 - 208
18	X-RAY DIFFRACTION	5	ALL	BBB	1001 - 1002
19	X-RAY DIFFRACTION	6	ALL	BBB	162 - 181

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