PDB-7o2u: PqsR (MvfR) in complex with antagonist 40

ID or keywords:

Entry

Database: PDB / ID: 7o2u

Title

PqsR (MvfR) in complex with antagonist 40

Components

LysR family transcriptional regulator

Keywords

DNA BINDING PROTEIN / Antagonist - receptor complex

Function / homology

Function and homology information

DNA-binding transcription factor activity
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 3 Å

Authors

Emsley, J. / Richardson, W.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: PqsR (MvfR) in complex with antagonist 40
Authors: Emsley, J. / Richardson, W.

History

Deposition	Mar 31, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7o2u.cif.gz	90 KB	Display	PDBx/mmCIF format
PDB format	pdb7o2u.ent.gz		Display	PDB format
PDBx/mmJSON format	7o2u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7o2u_validation.pdf.gz	701 KB	Display	wwPDB validaton report
Full document	7o2u_full_validation.pdf.gz	702.7 KB	Display
Data in XML	7o2u_validation.xml.gz	9.8 KB	Display
Data in CIF	7o2u_validation.cif.gz	12.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o2/7o2u ftp://data.pdbj.org/pub/pdb/validation_reports/o2/7o2u	HTTPS FTP

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Related structure data

Related structure data	4jvcS S: Starting model for refinement
Similar structure data	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: LysR family transcriptional regulator

hetero molecules

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

1

AAA: LysR family transcriptional regulator

hetero molecules

AAA: LysR family transcriptional regulator

hetero molecules

defined by author
Evidence: gel filtration
54.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	120.433, 120.433, 115.784
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	LysR family transcriptional regulator / Transcriptional regulator MvfR Mass: 26749.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mvfR, DY930_15985, E4V10_05145, F3H14_28375 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1C6ZJJ6
#2: Chemical	ChemComp-V0H / 2-[4-[(2S)-3-(6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanyl-propoxy]phenoxy]ethanenitrile / 2-[4-[(2~{S})-3-(6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanyl-propoxy]phenoxy]ethanenitrile Mass: 385.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₁₆ClN₃O₄ / Feature type: SUBJECT OF INVESTIGATION
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: 4.53 Å³/Da / Density % sol: 72.85 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Trisodium Citrate 200 mM Ammonium acetate 4-10% MPD PH range: pH 5.5-6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9159 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 21, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9159 Å / Relative weight: 1
Reflection	Resolution: 3→104.3 Å / Num. obs: 10259 / % possible obs: 99.1 % / Redundancy: 18.6 % / CC_1/2: 1 / Net I/σ(I): 17.3
Reflection shell	Resolution: 3→3.18 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1621 / CC_1/2: 0.887

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
DIALS		data reduction
Aimless		data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 4JVC

4jvc

Resolution: 3→77.614 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.935 / Cross valid method: FREE R-VALUE / ESU R: 0.475 / ESU R Free: 0.332
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.267	435	4.243 %
R_work	0.2218	9818	-
all	0.224	-	-
obs	-	10253	98.482 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 111.241 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.239 Å²	2.119 Å²	0 Å²
2-	-	4.239 Å²	0 Å²
3-	-	-	-13.75 Å²

Refinement step

Cycle: LAST / Resolution: 3→77.614 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1598	0	27	0	1625

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	1657
X-RAY DIFFRACTION	r_bond_other_d	0.035	0.017	1532
X-RAY DIFFRACTION	r_angle_refined_deg	1.302	1.636	2249
X-RAY DIFFRACTION	r_angle_other_deg	2.318	1.568	3540
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.003	5	202
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.148	21.429	91
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.556	15	275
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.45	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.047	0.2	215
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1850
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	361
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	347
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.22	0.2	1463
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	789
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.065	0.2	737
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.114	0.2	27
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.001	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.26	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.347	0.2	40
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.132	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	6.03	11.827	811
X-RAY DIFFRACTION	r_mcbond_other	6.026	11.823	809
X-RAY DIFFRACTION	r_mcangle_it	9.676	17.744	1012
X-RAY DIFFRACTION	r_mcangle_other	9.68	17.745	1012
X-RAY DIFFRACTION	r_scbond_it	5.417	12.33	846
X-RAY DIFFRACTION	r_scbond_other	5.414	12.33	847
X-RAY DIFFRACTION	r_scangle_it	8.834	18.288	1237
X-RAY DIFFRACTION	r_scangle_other	8.831	18.291	1238
X-RAY DIFFRACTION	r_lrange_it	13.939	138.425	1808
X-RAY DIFFRACTION	r_lrange_other	13.936	138.399	1809

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 (%)
3-3.078	0.404	28	0.433	703	X-RAY DIFFRACTION	98.9175
3.078-3.162	0.401	26	0.402	696	X-RAY DIFFRACTION	99.0398
3.162-3.254	0.354	24	0.369	684	X-RAY DIFFRACTION	99.1597
3.254-3.354	0.316	31	0.314	659	X-RAY DIFFRACTION	99.2806
3.354-3.464	0.434	21	0.309	640	X-RAY DIFFRACTION	99.2493
3.464-3.585	0.428	26	0.275	613	X-RAY DIFFRACTION	99.2236
3.585-3.72	0.303	32	0.274	598	X-RAY DIFFRACTION	98.9011
3.72-3.872	0.343	26	0.247	573	X-RAY DIFFRACTION	98.5197
3.872-4.044	0.257	19	0.234	558	X-RAY DIFFRACTION	98.9708
4.044-4.241	0.274	29	0.215	525	X-RAY DIFFRACTION	98.5765
4.241-4.47	0.223	23	0.178	501	X-RAY DIFFRACTION	98.1273
4.47-4.741	0.207	18	0.147	484	X-RAY DIFFRACTION	99.0138
4.741-5.068	0.184	21	0.162	460	X-RAY DIFFRACTION	97.5659
5.068-5.473	0.198	20	0.172	427	X-RAY DIFFRACTION	98.6755
5.473-5.994	0.311	20	0.19	386	X-RAY DIFFRACTION	98.0676
5.994-6.699	0.227	20	0.196	356	X-RAY DIFFRACTION	96.9072
6.699-7.731	0.189	12	0.184	320	X-RAY DIFFRACTION	97.076
7.731-9.458	0.287	20	0.153	271	X-RAY DIFFRACTION	97.651
9.458-13.331	0.237	11	0.163	222	X-RAY DIFFRACTION	95.4918
13.331-77.61	0.257	8		142	X-RAY DIFFRACTION	94.9367

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