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- PDB-7ff8: Pseudomonas aeruginosa Virulence Factor Regulator with cAMP ligan... -

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Basic information

Entry
Database: PDB / ID: 7ff8
TitlePseudomonas aeruginosa Virulence Factor Regulator with cAMP ligand and Cl(triethylphosphine)gold(I)
ComponentscAMP-activated global transcriptional regulator Vfr
KeywordsDNA BINDING PROTEIN / cAMP / auranofin / virulence / 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
: / triethylphosphanuidylgold(1+) / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP-activated global transcriptional regulator Vfr
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.2Mar 5, 2025Group: Database references / Refinement description / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / struct_ncs_dom_lim
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 / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id

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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)50,42817
Polymers47,6992
Non-polymers2,72915
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-112 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.264, 49.928, 62.381
Angle α, β, γ (deg.)90.000, 100.145, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 18 through 36 or (resid 37...
d_2ens_1(chain "B" and (resid 18 through 22 or (resid 23...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAGLNGLNAA18 - 11214 - 108
d_12SERSERPHEPHEAA115 - 211111 - 207
d_21ALAALAGLUGLUBB18 - 9814 - 94
d_22ARGARGPHEPHEBB108 - 211104 - 207

NCS oper: (Code: givenMatrix: (0.511813086334, -0.0408811818024, -0.858123588787), (-0.0374460523018, -0.99897940446, 0.0252575262284), (-0.858280349201, 0.0192062083349, -0.512821571052)Vector: 324. ...NCS oper: (Code: given
Matrix: (0.511813086334, -0.0408811818024, -0.858123588787), (-0.0374460523018, -0.99897940446, 0.0252575262284), (-0.858280349201, 0.0192062083349, -0.512821571052)
Vector: 324.898391907, 76.20708219, 571.446815648)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein cAMP-activated global transcriptional regulator Vfr


Mass: 23849.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Soaked with Chloro(triethylphosphine)gold(I) / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: vfr, PA0652 / Production host: Escherichia coli (E. coli) / Strain (production host): T1R / References: UniProt: P55222

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Non-polymers , 5 types, 15 molecules

#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-AUF / triethylphosphanuidylgold(1+) / gold(I)-triethylphosphane


Mass: 315.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15AuP / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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Details

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: 2.25 Å3/Da / Density % sol: 45.43 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 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: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1.04 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.8→42.3 Å / Num. obs: 21209 / % possible obs: 99.87 % / Redundancy: 2 % / Biso Wilson estimate: 47.29 Å2 / CC1/2: 0.975 / Net I/σ(I): 13.46
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 2078 / CC1/2: 0.351

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Processing

Software
NameVersionClassification
Coot0.8.9.2model building
PHENIX1.18.2_3874refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OZ6

2oz6


Resolution: 2.8→34.52 Å / SU ML: 0.4403 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3265 1079 5.27 %
Rwork0.2691 19388 -
obs0.2721 20467 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.72 Å2
Refinement stepCycle: LAST / Resolution: 2.8→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 87 0 2924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01012950
X-RAY DIFFRACTIONf_angle_d1.35273996
X-RAY DIFFRACTIONf_chiral_restr0.0588474
X-RAY DIFFRACTIONf_plane_restr0.0064495
X-RAY DIFFRACTIONf_dihedral_angle_d35.9595444
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.27402202151 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.41751200.33892432X-RAY DIFFRACTION99.8
2.93-3.080.34721460.30572424X-RAY DIFFRACTION99.88
3.08-3.270.36291650.30832395X-RAY DIFFRACTION99.88
3.27-3.530.35541300.28432430X-RAY DIFFRACTION99.96
3.53-3.880.311260.25932456X-RAY DIFFRACTION99.88
3.88-4.440.321210.22212428X-RAY DIFFRACTION99.92
4.44-5.590.28721140.26352443X-RAY DIFFRACTION100
5.59-34.520.31111570.26352380X-RAY DIFFRACTION99.06
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)
10.102638158198-0.0835624509055-0.08426600783060.3210501815170.2583256721660.07499937657480.0306430681721-0.01042325129510.131851560611-0.01353581113150.00157720990413-0.08706853508760.100771236028-0.0244083038621-0.0004742360657480.2227468467820.02530798601270.02874966398340.1754753403980.02825408186820.152405234963418.59076088620.8579076298136.251449736
20.1277564316320.06656914888190.02129559476750.0686192119008-0.07863121747240.100688109697-0.05114235787870.0104563995304-0.1540304731180.02972545145460.1877468807020.004004069238160.371648756654-0.07506303124650.1480923980380.33621820062-0.078634120217-0.01087264428540.3497502979870.0420864973307-0.0814462293706393.57070693123.8573875929137.306759765
30.176857437891-0.0630250429451-0.06571569207280.09929563549160.08326061955360.07727751981870.0008464370447110.258904914579-0.0136207147621-0.201299031086-0.0176116970197-0.195710566731-0.0840850249308-0.140164107204-0.05293223504490.147148642861-0.0333654472507-0.007402510094460.172041610035-0.0583677787750.354659857845421.04081540450.1784730944142.404686055
40.000446610307346-0.0246022667731-0.01317918710050.4116109750880.165599152720.223429853129-0.188512390231-0.00400057041607-0.0196100477853-0.120840108444-0.141540687942-0.0130136238627-0.02214861902720.0627862749867-0.5348825010.368687382462-0.267500157542-0.0311259546149-0.01550525867260.156495726020.383766142599407.56193306243.8827994878147.810366356
50.4224294583650.08618335268060.1341870832810.07539737125930.1486058034190.2897259930860.0989421935263-0.163504202966-0.0198149399635-0.0228466554839-0.285537957779-0.1563193181290.2982604138610.0142848318393-0.2699206928510.2540177489040.0441341467673-0.0777038594903-0.2112229640470.2600362026580.166529728043419.85479617844.41950167141.138877942
60.174429316311-0.07318975352130.2800102498460.2734251616070.1448952284680.592880477292-0.2604672718490.370357995234-0.0836290662515-0.252479725334-0.133767298257-0.2381793386030.246849726874-0.0739843894671-0.1989433353290.0823118338384-0.1444543873340.4387442724720.2746328247520.1598489259290.48407103892430.41501900644.8020825398134.43583671
70.08693792093240.123538552161-0.0160894561850.2093810672270.07410335536140.15961309750.0936588364916-0.0234327849859-0.02725241331790.1246648313990.0334684557805-0.7173627416460.07424463653240.183774004270.03261405683710.186367125179-0.02068582212590.05950183840.1609007149870.04050440854010.30144701008420.57623597431.7687661195144.679090613
80.004079042516030.00130340908831-0.009201554487410.0287209356505-0.01854751450310.0237489505304-0.0646410495198-0.1197066418670.0182260646792-0.01382934194670.076614862406-0.01425226010480.1073468651280.116999760887-0.06900931358490.4943833080440.07970979571830.2180788213160.668366913345-0.241407673190.500118994984405.59711090634.0018121716159.971279769
90.012587836452-0.0120300057736-0.01296904322220.287191860127-0.09366279367140.0507341716864-0.0445688991414-0.09108037984880.1247477727370.159912806919-0.00938835220717-0.0784085197885-0.09514444559820.01200793013510.0003151487217250.110877558403-0.0597377270781-0.1060733755110.568534309684-0.1822218164880.232357389385414.07634595943.4576600702170.193315855
100.0550324000973-0.0793050067357-0.01648826302890.128095473157-0.0001838802811820.254729670214-0.11112802465-0.1762688516620.1336447630510.06865611633730.0254499549871-0.213831559440.0059420862197-0.203851844768-0.270404577706-0.01387719899580.3087798941540.165114262120.355857443299-0.3020588332430.172556403711400.58860666143.459915619161.740797273
110.00786430253662-0.00669741039119-0.02024069595640.008062457853040.0210791986490.06301900326640.1019623726070.02971631058980.0414365528466-0.0605787761572-0.02376756363410.09414128819120.06271643449120.1010175566340.002760600948320.1595589413230.138565676408-0.0489664344160.907411176235-0.1380149499660.630412872249406.05300616642.8026414191172.405604481
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 140 )AA9 - 1401 - 126
22chain 'A' and (resid 141 through 211 )AA141 - 211127 - 197
33chain 'B' and (resid 18 through 54 )BH18 - 541 - 37
44chain 'B' and (resid 55 through 66 )BH55 - 6638 - 49
55chain 'B' and (resid 67 through 96 )BH67 - 9650 - 74
66chain 'B' and (resid 97 through 116 )BH97 - 11675 - 92
77chain 'B' and (resid 117 through 139 )BH117 - 13993 - 115
88chain 'B' and (resid 140 through 156 )BH140 - 156116 - 132
99chain 'B' and (resid 157 through 173 )BH157 - 173133 - 149
1010chain 'B' and (resid 174 through 198 )BH174 - 198150 - 174
1111chain 'B' and (resid 199 through 212 )BH199 - 212175 - 188

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