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- PDB-5xbt: The structure of BrlR bound to c-di-GMP -

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Basic information

Entry
Database: PDB / ID: 5xbt
TitleThe structure of BrlR bound to c-di-GMP
ComponentsProbable transcriptional regulator
KeywordsDNA BINDING PROTEIN / c-di-GMP / Receptor / HTH domain
Function / homology
Function and homology information


DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
Similarity search - Function
Integron-associated effector binding protein / Integron-associated effector binding protein / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / MerR family regulatory protein / Regulatory factor, effector binding domain superfamily / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance ...Integron-associated effector binding protein / Integron-associated effector binding protein / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / MerR family regulatory protein / Regulatory factor, effector binding domain superfamily / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-C2E / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.495 Å
AuthorsWang, F. / Qing, H. / Gu, L.
CitationJournal: Nat Commun / Year: 2018
Title: BrlR from Pseudomonas aeruginosa is a receptor for both cyclic di-GMP and pyocyanin.
Authors: Wang, F. / He, Q. / Yin, J. / Xu, S. / Hu, W. / Gu, L.
History
DepositionMar 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / 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 1.2Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable transcriptional regulator
B: Probable transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,52417
Polymers62,7112
Non-polymers3,81315
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint19 kcal/mol
Surface area30540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.924, 135.924, 94.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable transcriptional regulator


Mass: 31355.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA4878 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9HUT5

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Non-polymers , 5 types, 185 molecules

#2: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 3.48 Å3/Da / Density % sol: 64.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: Lithium sulfate, Sodium citrate tribasic, PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 29957 / % possible obs: 99.9 % / Redundancy: 7.3 % / Net I/σ(I): 27.22

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.495→38.813 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 1461 5.06 %
Rwork0.2124 --
obs0.2154 28884 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.946 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.0101 Å2-0 Å20 Å2
2---14.0101 Å20 Å2
3---28.0203 Å2
Refinement stepCycle: LAST / Resolution: 2.495→38.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 260 170 4854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094816
X-RAY DIFFRACTIONf_angle_d1.2576544
X-RAY DIFFRACTIONf_dihedral_angle_d16.2721792
X-RAY DIFFRACTIONf_chiral_restr0.077670
X-RAY DIFFRACTIONf_plane_restr0.006830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4947-2.58380.39231420.30332461X-RAY DIFFRACTION88
2.5838-2.68730.40541320.28782633X-RAY DIFFRACTION92
2.6873-2.80950.33091390.25722633X-RAY DIFFRACTION92
2.8095-2.95760.33671450.26672719X-RAY DIFFRACTION95
2.9576-3.14280.30481420.24132772X-RAY DIFFRACTION98
3.1428-3.38540.30571540.22422803X-RAY DIFFRACTION99
3.3854-3.72580.28281540.21942807X-RAY DIFFRACTION99
3.7258-4.26440.25461500.18932858X-RAY DIFFRACTION100
4.2644-5.37040.211520.17352860X-RAY DIFFRACTION100
5.3704-38.81820.24311510.20442877X-RAY DIFFRACTION99

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