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- PDB-6b8a: Crystal structure of MvfR ligand binding domain in complex with M64 -

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Basic information

Entry
Database: PDB / ID: 6b8a
TitleCrystal structure of MvfR ligand binding domain in complex with M64
ComponentsDNA-binding transcriptional regulator
KeywordsTRANSCRIPTION / MVFR TRANSCRIPTIONAL REGULATOR / PQSR
Function / homology
Function and homology information


regulation of transmembrane transport / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / extracellular region / plasma membrane
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CZG / COBALT HEXAMMINE(III) / LysR family transcriptional regulator / Multiple virulence factor regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKitao, T. / Steinbacher, S. / Maskos, K. / Blaesse, M. / Rahme, L.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI105902 and AI063433 United States
CitationJournal: MBio / Year: 2018
Title: Molecular Insights into Function and Competitive Inhibition ofPseudomonas aeruginosaMultiple Virulence Factor Regulator.
Authors: Kitao, T. / Lepine, F. / Babloudi, S. / Walte, F. / Steinbacher, S. / Maskos, K. / Blaesse, M. / Negri, M. / Pucci, M. / Zahler, B. / Felici, A. / Rahme, L.G.
History
DepositionOct 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding transcriptional regulator
B: DNA-binding transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7136
Polymers45,5502
Non-polymers1,1634
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-5 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.556, 121.524, 112.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DNA-binding transcriptional regulator / Transcriptional regulator / Transcriptional regulator MvfR


Mass: 22774.854 Da / Num. of mol.: 2 / Fragment: COINDUCER BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: mvfR, AO964_20870, AOY09_01875, B0B20_09895, PAERUG_E15_London_28_01_14_10887, PAERUG_P32_London_17_VIM_2_10_11_05492, PAMH19_4335
Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZLE6, UniProt: Q9I4X0*PLUS
#2: Chemical ChemComp-CZG / 2-[(5-nitro-1H-benzimidazol-2-yl)sulfanyl]-N-(4-phenoxyphenyl)acetamide


Mass: 420.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H16N4O4S
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 4.15 Å3/Da / Density % sol: 70.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 31% MPD, 90 mM imidazole pH 8.0, 180mM MgCl2, 10mM Co(NH3)6Cl3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→81.78 Å / Num. obs: 21542 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.46
Reflection shellResolution: 2.65→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 4980 / % possible all: 95.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0005refinement
REFMAC5.2.0005phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JVD

4jvd


Resolution: 2.65→81.78 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 21.897 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.273 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25113 863 4 %RANDOM
Rwork0.21637 ---
obs0.2178 20678 96.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 85.283 Å2
Baniso -1Baniso -2Baniso -3
1-4.34 Å20 Å20 Å2
2--2.16 Å20 Å2
3----6.5 Å2
Refinement stepCycle: LAST / Resolution: 2.65→81.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 74 17 3286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223333
X-RAY DIFFRACTIONr_bond_other_d0.0020.023042
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9954540
X-RAY DIFFRACTIONr_angle_other_deg0.9437030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33123.506154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22415551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6451528
X-RAY DIFFRACTIONr_chiral_restr0.0710.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02703
X-RAY DIFFRACTIONr_nbd_refined0.170.2561
X-RAY DIFFRACTIONr_nbd_other0.1360.22904
X-RAY DIFFRACTIONr_nbtor_refined0.160.21571
X-RAY DIFFRACTIONr_nbtor_other0.0770.22001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.89622602
X-RAY DIFFRACTIONr_mcbond_other0.3082816
X-RAY DIFFRACTIONr_mcangle_it2.40933271
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.45241522
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.98261263
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.653→2.722 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.531 57 -
Rwork0.447 1477 -
obs--94.34 %
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)
14.67071.3211-0.33165.39810.73985.4644-0.0112-0.108-0.13550.3145-0.1206-0.76150.11420.76010.1317-0.17850.0664-0.0149-0.00170.09950.049534.719-10.1977.643
25.43921.3181-0.40685.05890.8776.3321-0.37750.3667-0.3162-0.66670.1595-0.09670.4973-0.15680.2180.04670.0760.1019-0.0212-0.01750.038219.606-25.88-4.806
35.98613.57540.81234.7535-1.78296.9220.03530.33290.02890.11050.03130.50230.3098-0.754-0.0665-0.00370.0740.07550.05870.01270.06597.39-31.11718.25
44.27020.46221.36286.8567-1.70915.55880.1472-0.3932-0.13890.8999-0.3415-0.2968-0.34310.46680.19440.06170.0292-0.0269-0.01840.08430.019927.638-22.67729.873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A93 - 166
2X-RAY DIFFRACTION1A265 - 295
3X-RAY DIFFRACTION2A167 - 264
4X-RAY DIFFRACTION3B94 - 166
5X-RAY DIFFRACTION3B265 - 295
6X-RAY DIFFRACTION4B167 - 264

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