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- PDB-5xql: Crystal structure of a Pseudomonas aeruginosa transcriptional reg... -

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Basic information

Entry
Database: PDB / ID: 5xql
TitleCrystal structure of a Pseudomonas aeruginosa transcriptional regulator
ComponentsMultidrug-efflux transporter 1 regulator
KeywordsTRANSCRIPTION / Pseudomonas aeruginosa / transcriptional regulator
Function / homology
Function and homology information


DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / nucleotide binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding
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 / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. ...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 / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-C2E / Transcriptional regulator / Transcriptional regulator BrlR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.494 Å
AuthorsRaju, H. / Sharma, R.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of BrlR with c-di-GMP
Authors: Raju, H. / Sharma, R.
History
DepositionJun 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 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

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Assembly

Deposited unit
A: Multidrug-efflux transporter 1 regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8213
Polymers33,4401
Non-polymers1,3812
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-1 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.944, 135.944, 95.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Multidrug-efflux transporter 1 regulator / Transcriptional regulator


Mass: 33439.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: bmrR, AO964_25340, AOY09_00728, B0B20_02615, PAERUG_E15_London_28_01_14_00871, PAERUG_P32_London_17_VIM_2_10_11_01154
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q416, UniProt: Q9HUT5*PLUS
#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


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2

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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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 6.5 / Details: 0.15 M Mg Cl2, 0.1 M Bis-Tris pH 6.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.49→35.07 Å / Num. obs: 12920 / % possible obs: 81.4 % / Redundancy: 3.6 % / Net I/σ(I): 20.8

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Processing

Software
NameVersionClassification
PHENIXdev_2747refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.494→35.051 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.37
RfactorNum. reflection% reflection
Rfree0.2745 648 5.02 %
Rwork0.2323 --
obs0.2345 12913 81.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.494→35.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 92 0 2286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062356
X-RAY DIFFRACTIONf_angle_d0.9193215
X-RAY DIFFRACTIONf_dihedral_angle_d26.072892
X-RAY DIFFRACTIONf_chiral_restr0.06333
X-RAY DIFFRACTIONf_plane_restr0.007409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4936-2.68610.3831700.31051303X-RAY DIFFRACTION44
2.6861-2.95630.3966980.3052040X-RAY DIFFRACTION69
2.9563-3.38370.30261420.26522802X-RAY DIFFRACTION94
3.3837-4.2620.26441760.21892988X-RAY DIFFRACTION100
4.262-35.05470.22771620.19693132X-RAY DIFFRACTION99
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)
10.1690.14610.01260.4231-0.00540.00210.0533-0.2509-0.09540.3343-0.14810.08510.07880.0829-0.15020.43590.00160.20150.2190.0490.2825220.2214159.077344.1208
23.60051.77380.58640.91090.34560.18380.14220.285-0.1853-0.3011-0.0306-0.0684-0.01470.0248-0.00490.46420.1299-0.01720.1758-0.00540.2646203.9455131.231631.2596
30.9361-0.4040.23511.8133-0.16030.5974-0.02250.07170.3103-0.11380.0158-0.1996-0.1437-0.0248-0.01620.1989-0.00060.00640.13950.05240.2487164.247132.344417.1187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 270 )

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