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- PDB-3eq2: Structure of Hexagonal Crystal form of Pseudomonas aeruginosa RssB -

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Basic information

Entry
Database: PDB / ID: 3eq2
TitleStructure of Hexagonal Crystal form of Pseudomonas aeruginosa RssB
ComponentsProbable two-component response regulator
KeywordsSIGNALING PROTEIN / Adaptor SigmaS
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / metal ion binding / cytosol
Similarity search - Function
: / L1 transposable element, trimerization domain / Stage II sporulation protein E (SpoIIE) / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Transcriptional regulatory protein WalR-like / Response regulator receiver domain ...: / L1 transposable element, trimerization domain / Stage II sporulation protein E (SpoIIE) / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 4-Layer Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable two-component response regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.401 Å
AuthorsLevchenko, I. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
CitationJournal: To be Published
Title: The structure of rssb, a clpx adaptor protein that regulates sigma S
Authors: Levchenko, I. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
History
DepositionSep 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable two-component response regulator
B: Probable two-component response regulator


Theoretical massNumber of molelcules
Total (without water)87,9032
Polymers87,9032
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-29 kcal/mol
Surface area39230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.277, 76.277, 305.077
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Probable two-component response regulator


Mass: 43951.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA2798, rssb / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I045

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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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.1 M Na Cacodylate, 0.2M NaCl, 4% PEG 8000, 8.2 mg/ml protein, cryo-protected with 25% glycerol , pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2008 / Details: crystal monochrometer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twinType: merohedral / Operator: k,h,-l / Fraction: 0.509
ReflectionResolution: 3.4→50 Å / Num. obs: 26199 / % possible obs: 95.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.15 / Χ2: 0.919 / Net I/σ(I): 7.941
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.4-3.523.50.57825810.4295.3
3.52-3.663.60.39526660.47295.5
3.66-3.833.50.28326180.51895.5
3.83-4.033.50.22626110.56895.5
4.03-4.283.60.16725980.67595.6
4.28-4.613.60.12725950.89595.5
4.61-5.083.60.11726870.99896.1
5.08-5.813.60.13125870.98395.8
5.81-7.323.60.13926321.28696
7.32-503.50.07426242.38195

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
PHENIXrefinement
RefinementResolution: 3.401→29.046 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1338 5.12 %random
Rwork0.271 ---
obs0.272 26130 95.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.003 Å2 / ksol: 0.253 e/Å3
Displacement parametersBiso max: 346.02 Å2 / Biso mean: 109.898 Å2 / Biso min: 34.04 Å2
Baniso -1Baniso -2Baniso -3
1--33.292 Å20 Å2-0 Å2
2---33.292 Å20 Å2
3----27.717 Å2
Refinement stepCycle: LAST / Resolution: 3.401→29.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 0 0 5536

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