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- PDB-7ff0: Pseudomonas aeruginosa Virulence Factor Regulator with cAMP ligan... -

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Basic information

Entry
Database: PDB / ID: 7ff0
TitlePseudomonas aeruginosa Virulence Factor Regulator with cAMP ligand and auranofin
ComponentscAMP-activated global transcriptional regulator Vfr
KeywordsDNA 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
helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site ...helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP-activated global transcriptional regulator Vfr
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChew, B.L.A. / Luo, D.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)2016-T2-2-097 Singapore
CitationJournal: 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
DepositionJul 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 7, 2024Group: 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
Revision 1.3Mar 5, 2025Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP-activated global transcriptional regulator Vfr
B: cAMP-activated global transcriptional regulator Vfr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,46310
Polymers48,1272
Non-polymers1,3368
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-79 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.600, 49.643, 63.915
Angle α, β, γ (deg.)90.000, 100.374, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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
IDModelComponents
11B-302-

SO4

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Components

#1: Protein cAMP-activated global transcriptional regulator Vfr


Mass: 24063.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Soaking with Auranofin / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: vfr / Production host: Escherichia coli (E. coli) / Strain (production host): T1R / References: UniProt: P55222
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.55 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.6M AMMONIUM SULPHATE, 0.1M BICINE

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 R 300K-W / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→43 Å / Num. obs: 23447 / % possible obs: 98.99 % / Redundancy: 1.9 % / Biso Wilson estimate: 30.28 Å2 / CC1/2: 0.986 / Net I/σ(I): 3.8
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 1273 / CC1/2: 0.653

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OZ6

2oz6


Resolution: 2.6→42.12 Å / SU ML: 0.3323 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 23.5699
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2391 1201 5.12 %
Rwork0.2069 22246 -
obs0.2085 23447 92.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.63 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 26 166 3357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01173229
X-RAY DIFFRACTIONf_angle_d1.52224358
X-RAY DIFFRACTIONf_chiral_restr0.0786499
X-RAY DIFFRACTIONf_plane_restr0.009550
X-RAY DIFFRACTIONf_dihedral_angle_d44.95470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70.31471230.28052377X-RAY DIFFRACTION89.86
2.7-2.830.31611310.26472445X-RAY DIFFRACTION92.4
2.83-2.980.2561250.24922506X-RAY DIFFRACTION93.3
2.98-3.160.27281390.23482490X-RAY DIFFRACTION93.33
3.16-3.410.27551450.20492467X-RAY DIFFRACTION93.49
3.41-3.750.20971370.18612474X-RAY DIFFRACTION93.08
3.75-4.290.19321360.16442453X-RAY DIFFRACTION92.73
4.29-5.40.20751050.16642442X-RAY DIFFRACTION90.71
5.41-42.120.23471600.22592592X-RAY DIFFRACTION98.04
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.6950778522160.02295510748370.03597643662990.0998072151831-0.2892010184620.2404857104910.1614780436330.4212202243120.385437013406-1.008103588460.108775626858-0.0731234539994-0.2788657818040.02916522844131.272121560610.277746723720.2649400184390.6331681353720.28343499653-0.48627524768-0.42605137063148.28399730713.387132556464.9570840273
20.119560432023-0.109091576508-0.09756039281540.151726472413-0.04053007547240.1553492675250.18533871147-0.386057426167-0.670753646-0.112548953957-0.13460529731-0.01112392637770.2778286393510.05558727224880.1574381386070.1885468038240.005376137145230.01353216374260.1837794882360.04789958289290.0860744082512142.8710670998.8385939884682.1174404058
31.215290079640.0637754221892-0.2430467750541.62029133071-0.3186183165510.3714660224030.119315234085-0.2161316222330.1837192020620.0462945061781-0.08674182309830.0212939379431-0.0316877530459-0.05673569620480.01370688855290.1609472162940.0209988572116-0.006670516882120.15678530467-0.0003486035422060.135854474437140.65795550916.403716150780.6400772568
40.120263198354-0.01916534228270.08858321545870.2129313757230.1918220734550.3614541019850.4611227612890.01691633309150.31685756551-0.0245998426862-0.2046192283760.09369772464070.7898033202810.3379469425490.05926738418910.181712644610.1215796471050.03404839217790.3686368519410.02809550676230.262666190769153.92182512916.235945573470.6949333846
50.016698072744-0.282335631761-0.1697073186810.369274036584-0.1465178578280.2897451117670.0323613647442-0.124137070609-0.29130145928-0.18148405536-0.1095459399410.0977193079291-0.106970003956-0.00717903231689-0.04577594790650.1821449531390.01735202288850.008655691236930.158223855915-0.006452798770470.171719873173139.07174000328.936452404177.1360504006
60.06413693909510.09206092291190.1205066916140.2926938599090.08467732073440.102648638939-0.343588668834-0.3196771756940.2739619124060.0640770643129-0.2470633766020.025125733160.3316383226170.0640903682789-0.05360140032070.197010976740.0616603207592-0.0206655087290.217090206158-0.01631321594570.143102449232121.623071726.999648788179.4864602187
70.273965027798-0.1544252286440.07937511360710.0738888327884-0.2099821675550.248036771329-0.5852351608620.331240803019-0.0651659411683-0.004864296837090.157859501446-0.006108299138080.651184021604-0.0215920113615-0.1094668778610.578508220742-0.0109864036203-0.02609868646090.32694343378-0.08245857201580.264811110795121.00732109419.411390426167.871216642
80.4146288950410.237565580013-0.03981000896990.1075986356530.07450780313670.561516589163-0.618230107319-0.210701931448-0.6718492519170.135362717540.1439967791870.1522939769510.7695937845540.143587524846-0.07225267359020.217101340219-0.0426743634202-0.01574646319650.2280560411340.008126782739650.230911736155117.07963824918.617808832684.6481544303
90.102373576478-0.0412550577260.06253537328190.0505910273532-0.1127707799670.0935811356734-0.2704589160110.186904600785-0.103162093644-0.1003874862230.03937925018540.5473475333110.356139848684-0.8460706048640.001211665445280.496156119624-0.06908938792120.00182133120280.476913409524-0.1002192613120.386016517319114.43424681420.519840157471.7478798858
100.871966460559-0.369191661439-0.132353447450.7800613355970.5374910698850.7402907175330.1582366506461.105904864280.0110146644888-0.4019890862760.136122649566-0.533451357487-0.3701085846740.1124287420350.2528836245520.239526501183-0.08593898187330.0799860016176-0.05229511305730.003736854384470.306885843279149.31642008947.912282951179.4767552499
111.933652285340.7787955394410.009992974382291.47753309723-0.1312956204690.338850351377-0.287637458458-0.334559894084-0.0603240504727-0.2008273515030.10091371429-0.1551882952310.03045541867970.0701004591179-0.3072336123490.13089963302-0.02242457972590.004313419830470.09109210040090.01262933840110.150640324056141.88716129240.999779424682.8477751689
120.440213482458-0.2714770240940.3824847736110.1742246444260.1266309959321.30667723982-0.3354627030270.112182811260.336444771902-0.5499990896330.0123732509119-0.484464368653-0.270083132409-0.45535116754-0.1725845169860.346098509146-0.2087981111320.2409171700060.2962994316140.04301637318760.212979793659153.98308336541.330729378871.9331936921
130.11638428013-0.023480731519-0.08789100916260.429351438677-0.1623889956730.2384457801890.1276800694510.156574886699-0.2384607300710.241881242865-0.0963502974765-0.4533036062-0.32699540995-0.0255373729057-0.01287196143370.201690370610.004917051296260.0135615696520.132155144810.0143162135230.287619542837146.31479762828.564508090483.7842139495
140.679595484746-0.1323628978990.2415906011780.456571373841-0.3345039148260.2015474766240.218922628851-0.118181247193-0.0410734958347-0.06277347387150.0538793770857-0.07842528050210.1888271506180.1282892837010.00218539465530.233836721214-0.00188727331669-0.004910198035960.271112531464-0.05998887247690.20774208539133.25644182537.2120524065104.113976092
150.155960566184-0.126374017785-0.2623614349170.733807391357-0.5057003971010.9091293212860.136783945809-0.2049449503260.239662785243-0.8779615856120.256151161011-0.108619336962-0.160817933922-0.4401578678170.141650697132-0.178190422336-0.0427656121590.03893247605340.472164320276-0.09627649445360.29621894931126.81634907138.6674782109109.177088061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 115 )
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 141 )
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 157 )
7X-RAY DIFFRACTION7chain 'A' and (resid 158 through 173 )
8X-RAY DIFFRACTION8chain 'A' and (resid 174 through 197 )
9X-RAY DIFFRACTION9chain 'A' and (resid 198 through 214 )
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 39 )
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 96 )
12X-RAY DIFFRACTION12chain 'B' and (resid 97 through 114 )
13X-RAY DIFFRACTION13chain 'B' and (resid 115 through 139 )
14X-RAY DIFFRACTION14chain 'B' and (resid 140 through 184 )
15X-RAY DIFFRACTION15chain 'B' and (resid 185 through 214 )

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