PDB-7few: Pseudomonas aeruginosa Virulence Factor Regulator with cAMP ligan...

ID or keywords:

Entry

Database: PDB / ID: 7few

Title

Pseudomonas aeruginosa Virulence Factor Regulator with cAMP ligand and auranofin gold analogues

Components

(cAMP-activated global transcriptional regulator Vfr) x 2

Keywords

DNA BINDING PROTEIN /

cyclic AMP receptor protein

Function / homology

Function and homology information

DNA-binding transcription repressor activity / DNA-binding transcription activator activity /

cAMP binding /

protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of DNA-templated transcription /

cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Chew, B.L.A. / Luo, D.

Funding support

Singapore, 1items

Citation

Journal: Comput Struct Biotechnol J / Year: 2023
Title: Structural basis for the inhibitory mechanism of auranofin and gold(I) analogues against Pseudomonas aeruginosa global virulence factor regulator Vfr.
Authors: Zhang, Y. / Chew, B.L.A. / Wang, J. / Yuan, M. / Yam, J.K.H. / Luo, D. / Yang, L.

History

Deposition	Jul 22, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 27, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Feb 7, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7few.cif.gz	217.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7few.ent.gz	144.7 KB	Display	PDB format
PDBx/mmJSON format	7few.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fe/7few ftp://data.pdbj.org/pub/pdb/validation_reports/fe/7few	HTTPS FTP

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Related structure data

Related structure data	7ff0C 2oz6S S: Starting model for refinement C: citing same article (ref.)
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
Related items in Molecule of the Month	#48 - Dec 2003 Catabolite Activator Protein similarity (15) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (9) #251 - Nov 2020 Adenylyl Cyclase similarity (8)

Deposited unit

A: cAMP-activated global transcriptional regulator Vfr

B: cAMP-activated global transcriptional regulator Vfr

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	135.270, 49.553, 64.384
Angle α, β, γ (deg.)	90.000, 100.115, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	B-306- SO4

#1: Protein	cAMP-activated global transcriptional regulator Vfr Mass: 24063.729 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: vfr / Plasmid: 209E6 / Production host: Escherichia coli (E. coli) / Strain (production host): T1R / References: UniProt: P55222
#2: Protein	cAMP-activated global transcriptional regulator Vfr Mass: 24049.701 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: vfr / Plasmid: 209E6 / Production host: Escherichia coli (E. coli) / Strain (production host): T1R / References: UniProt: P55222
#3: Chemical	ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₂N₅O₆P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H₂O
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: 2.21 Å³/Da / Density % sol: 44.28 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.6 M Ammonium Sulphate, 0.1 M Bicine pH 9.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9762 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 13, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.75→33.29 Å / Num. obs: 81214 / % possible obs: 98 % / Redundancy: 2 % / B_iso Wilson estimate: 21.45 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.02433 / Net I/σ(I): 17.07
Reflection shell	Resolution: 1.75→1.81 Å / Num. unique obs: 3593 / CC_1/2: 0.649

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PHENIX	1.17.1_3660	refinement
HKL-3000		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2OZ6

2oz6

Resolution: 1.75→33.29 Å / SU ML: 0.1866 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6931
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2013	4099	5.05 %
R_work	0.1772	77115	-
obs	0.1784	81214	97.77 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 30.79 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→33.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3210	0	45	340	3595

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0066	3302
X-RAY DIFFRACTION	f_angle_d	0.8487	4456
X-RAY DIFFRACTION	f_chiral_restr	0.051	504
X-RAY DIFFRACTION	f_plane_restr	0.0041	558
X-RAY DIFFRACTION	f_dihedral_angle_d	35.3562	472

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 (%)
1.75-1.77	0.3457	117	0.2992	2222	X-RAY DIFFRACTION	79.97
1.77-1.79	0.3171	130	0.2824	2300	X-RAY DIFFRACTION	85.05
1.79-1.81	0.2806	132	0.2651	2426	X-RAY DIFFRACTION	90.36
1.81-1.84	0.2401	156	0.2401	2532	X-RAY DIFFRACTION	92.02
1.84-1.86	0.2341	132	0.2332	2562	X-RAY DIFFRACTION	96.04
1.86-1.89	0.2808	120	0.2308	2734	X-RAY DIFFRACTION	98.31
1.89-1.92	0.2551	134	0.2125	2671	X-RAY DIFFRACTION	99.86
1.92-1.95	0.2361	126	0.2	2775	X-RAY DIFFRACTION	99.97
1.95-1.98	0.2307	171	0.1772	2680	X-RAY DIFFRACTION	99.96
1.98-2.01	0.2251	116	0.1823	2723	X-RAY DIFFRACTION	99.93
2.01-2.05	0.1726	183	0.1731	2760	X-RAY DIFFRACTION	100
2.05-2.09	0.2001	140	0.1754	2683	X-RAY DIFFRACTION	100
2.09-2.13	0.2405	149	0.1789	2696	X-RAY DIFFRACTION	100
2.13-2.18	0.2003	151	0.1659	2710	X-RAY DIFFRACTION	99.97
2.18-2.23	0.2199	157	0.1719	2682	X-RAY DIFFRACTION	99.93
2.23-2.29	0.2161	155	0.1718	2723	X-RAY DIFFRACTION	99.9
2.29-2.35	0.2203	138	0.1708	2709	X-RAY DIFFRACTION	100
2.35-2.42	0.2213	142	0.1768	2706	X-RAY DIFFRACTION	99.82
2.42-2.5	0.2229	129	0.1738	2760	X-RAY DIFFRACTION	99.93
2.5-2.58	0.2023	168	0.1808	2704	X-RAY DIFFRACTION	99.97
2.58-2.69	0.2231	145	0.18	2702	X-RAY DIFFRACTION	99.93
2.69-2.81	0.1833	122	0.177	2734	X-RAY DIFFRACTION	99.76
2.81-2.96	0.206	137	0.1741	2728	X-RAY DIFFRACTION	99.83
2.96-3.14	0.1822	173	0.1732	2688	X-RAY DIFFRACTION	99.76
3.14-3.39	0.1981	156	0.1643	2688	X-RAY DIFFRACTION	99.75
3.39-3.73	0.181	100	0.1577	2732	X-RAY DIFFRACTION	99.37
3.73-4.26	0.1605	133	0.1457	2735	X-RAY DIFFRACTION	99.48
4.26-5.37	0.1759	143	0.1623	2696	X-RAY DIFFRACTION	99.16
5.37-33.29	0.1825	144	0.1973	2654	X-RAY DIFFRACTION	97.87

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	0.0137539411675	0.0830398558026	-0.200415171291	-0.0113004007955	-0.122271624897	0.116605555006	-0.107224266795	0.118189371828	-0.274740150721	-0.278227506825	0.0441234061817	-0.382377890352	0.0943856478313	0.0428260466352	0.168058667451	0.252023795323	0.0142630483109	0.0874995669647	0.24867506757	-0.0710990238688	0.256305426758	407.640389062	15.5782382314	129.133633832
2	-0.0158920470391	0.05952586515	0.0461056604907	0.108272479907	-0.195246952486	0.169369182256	0.245281136818	0.0993332611281	-0.0465830997556	0.164771391276	-0.0242187728202	-0.0143145167542	0.16415848012	0.139398208564	0.00177023061624	0.16121494461	0.017146266776	-0.0349850130829	0.133830209157	0.00256063594486	0.142777942882	401.552096026	11.7204727406	145.988388309
3	0.564650216487	0.184164024941	0.189162530351	0.743711307256	-0.042355938526	0.154052678641	0.0481579390316	-0.0434307878881	-0.0213150919985	0.066963428381	-0.0288584991847	0.124485447425	0.0407037191306	-0.0237923778476	-0.00167154969707	0.156156242453	0.0106086586655	0.00238728245038	0.147934161984	0.0137281077035	0.133395483099	395.180573351	18.6883859313	144.650910777
4	0.368189472245	-0.156287363785	-0.347139216176	0.6415777479	-0.332833877239	0.355127112701	0.0971227931757	-0.0100239138941	0.0330894144171	-0.00919116530286	-0.0486537125916	-0.117464604938	0.00252179774593	0.0315153234736	0.00488323302585	0.148723603205	0.0143908898953	-0.00664469937839	0.110980105191	0.00913178612269	0.123579697918	404.366820832	19.871881697	144.772526729
5	0.17362090156	-0.263867405126	-0.00577025714403	0.26304894682	-0.0421848112023	0.185654199766	-0.102464950299	0.0958345294578	0.0832638557842	-0.0297752846506	0.116153041834	-0.0117991662503	0.183699200637	0.175201946367	-0.000440798683402	0.168703265203	0.0333574180069	-0.00151889490068	0.242913680501	0.00561476170398	0.191134706904	412.93640882	18.7343614487	134.885457738
6	0.171055803387	0.000210374872327	0.21474599558	0.165429996982	0.205143373351	0.19148889541	-0.051793451388	0.00585776941557	-0.00138003844486	-0.105627512355	-0.006582124185	0.0487782999963	0.101193749906	-0.0401748159613	1.18017464407E-5	0.173771276077	0.0177734680094	0.0110205098747	0.12489722397	0.0118703403003	0.166770359848	398.845852368	31.7352735969	140.91426164
7	0.0451946348903	-0.0475540219224	0.00674398075957	0.176577325284	-0.112353417181	0.0681650573937	-0.00487205861796	-0.0329937127722	0.0742819981081	-0.156870098562	-0.0133517734296	0.143068634836	0.118111092107	-0.0186939008297	0.000243043005369	0.202808178246	0.00174446998205	-0.0328519761709	0.212938294576	-0.00856883706215	0.167869006073	380.688048607	29.8383756429	143.519104198
8	0.0896921862465	0.118893843668	-0.105690789583	0.133970108619	-0.139344069197	0.0822078883918	-0.401092026898	0.280689047617	-0.175462621107	-0.295901370715	0.147642214414	-0.234782049161	1.22427777342	-0.227207777409	-0.0332740761849	0.412563963717	-0.0568016988879	-0.0199413352137	0.286000352416	-0.0294738505877	0.161528895626	380.081886735	22.1772423907	131.684019767
9	0.462756311611	0.153989152317	-0.100378925989	0.498702217088	-0.0785304225716	0.577265036915	-0.147642719348	-0.0707144053302	-0.0797167988943	-0.216038636316	0.00890769539105	-0.0719690348484	0.293490323059	-0.194568653502	-0.0112534264776	0.225401638445	-0.0390464939611	0.0275851582506	0.230906194421	0.00843020648085	0.174813846402	375.139719177	22.0913945184	143.244371672
10	0.164553313039	0.169706720979	0.117220023064	0.443706209872	-0.066004975274	0.338020729653	-0.0905168707915	0.0344209780429	-0.0502615443717	-0.243618829397	0.0365355638691	-0.129513362683	-0.192944951844	0.0953319356606	-0.0164681244491	0.188422433534	-0.0473993115909	0.0337313165795	0.156220726382	-0.00195787618602	0.206098812858	409.767990208	49.8685107414	142.990081299
11	0.801787693299	0.552034737808	-0.238595555143	1.6805943846	0.000961764228673	0.859912597898	-0.0692195970351	-0.0158180014195	-0.0577565017766	-0.152591712572	0.0449763076907	-0.121403452395	-0.00702112192998	0.0220610598218	-0.0317082894543	0.129972299839	0.000583462262024	0.0211089063866	0.103275161231	0.0101179483732	0.143115988971	404.610219159	40.4545712116	144.688994721
12	0.950221235852	0.292220806919	0.318247822888	0.865985297718	-0.377202021275	0.990944309042	0.134563909217	-0.239678079081	-0.00738385056581	-0.00253692400401	-0.133495700875	0.00898755008687	-0.000410800449478	-0.111990233493	-0.0176991557773	0.120413836534	-0.0250129257729	-0.00373959228159	0.238904054406	-0.0247487961053	0.165412472304	389.561629327	40.6956247538	169.893080291

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 39 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 40 through 67 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 68 through 96 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 97 through 114 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 115 through 141 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 142 through 157 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 158 through 173 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 174 through 214 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 11 through 39 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 40 through 139 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 140 through 213 )

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