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- PDB-5yc9: Crystal structure of a Pseudomonas aeruginosa transcriptional reg... -

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Basic information

Entry
Database: PDB / ID: 5yc9
TitleCrystal structure of a Pseudomonas aeruginosa transcriptional regulator
ComponentsC-di-GMP-binding multidrug transporter transcriptional regulator BrlR
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 / negative regulation of DNA-templated transcription / nucleotide binding / 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
Transcriptional regulator / Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHarikiran, R. / Rohan, S.
CitationJournal: To Be Published
Title: Crystal structure of a Pseudomonas aeruginosa transcriptional regulator
Authors: Harikiran, R. / Sundararajan, R. / Sharma, R.
History
DepositionSep 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: C-di-GMP-binding multidrug transporter transcriptional regulator BrlR
B: C-di-GMP-binding multidrug transporter transcriptional regulator BrlR
C: C-di-GMP-binding multidrug transporter transcriptional regulator BrlR
D: C-di-GMP-binding multidrug transporter transcriptional regulator BrlR


Theoretical massNumber of molelcules
Total (without water)133,7594
Polymers133,7594
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14320 Å2
ΔGint-68 kcal/mol
Surface area53420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.642, 111.642, 261.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
C-di-GMP-binding multidrug transporter transcriptional regulator BrlR / Multidrug-efflux transporter 1 regulator / Transcriptional regulator


Mass: 33439.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: bmrR, brlR, AO964_25340, AOY09_00728, CAZ10_02115, CGU42_14110, CWI21_27955, PAERUG_E15_London_28_01_14_00871, RW109_RW109_06470
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q416, UniProt: Q9HUT5*PLUS

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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: 3.51 Å3/Da / Density % sol: 69.31 %
Description: the entry contains Friedel pairs in I_Plus/Minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% v/v 1,4-Dioxane, 0.1 M MES pH 6.5, 1.6 M Ammonium sulfate

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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: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. obs: 60294 / % possible obs: 100 % / Redundancy: 7.9 % / Net I/σ(I): 18.71
Reflection shellResolution: 2.9→2.95 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2875)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→34.323 Å / Cross valid method: FREE R-VALUE / σ(F): 56.84 / Phase error: 33.88 / Stereochemistry target values: TWIN_LSQ_F
Details: the entry contains Friedel pairs in I_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.3069 3949 6.55 %
Rwork0.268 --
obs0.2715 60294 74.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→34.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8290 0 0 0 8290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9058-2.95590.4168340.3862577X-RAY DIFFRACTION14
2.9559-3.00960.4219510.3621811X-RAY DIFFRACTION20
3.0096-3.06740.3738700.37871186X-RAY DIFFRACTION30
3.0674-3.12990.4135890.35071703X-RAY DIFFRACTION43
3.1299-3.19790.40791100.34812083X-RAY DIFFRACTION51
3.1979-3.27220.39661260.32242146X-RAY DIFFRACTION54
3.2722-3.35390.34481290.31862307X-RAY DIFFRACTION58
3.3539-3.44440.33381450.31452522X-RAY DIFFRACTION64
3.4444-3.54550.34121880.2862923X-RAY DIFFRACTION73
3.5455-3.65980.35211950.28183348X-RAY DIFFRACTION83
3.6598-3.79030.27172230.26873696X-RAY DIFFRACTION91
3.7903-3.94160.25242100.27313735X-RAY DIFFRACTION93
3.9416-4.12050.35552120.26373763X-RAY DIFFRACTION94
4.1205-4.3370.30992120.25323743X-RAY DIFFRACTION94
4.337-4.60760.30122150.22843782X-RAY DIFFRACTION94
4.6076-4.96160.252140.21553741X-RAY DIFFRACTION94
4.9616-5.45770.27432120.2533793X-RAY DIFFRACTION94
5.4577-6.23990.34222260.28363796X-RAY DIFFRACTION94
6.2399-7.83360.24992140.26793722X-RAY DIFFRACTION94
7.8336-28.17930.29411970.25673605X-RAY DIFFRACTION90

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