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- PDB-3f6p: Crystal Structure of unphosphorelated receiver domain of YycF -

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Basic information

Entry
Database: PDB / ID: 3f6p
TitleCrystal Structure of unphosphorelated receiver domain of YycF
ComponentsTranscriptional regulatory protein yycF
KeywordsTRANSCRIPTION REGULATOR / unphosphorelated / receiver domain / Cytoplasm / DNA-binding / Phosphoprotein / Transcription / Transcription regulation / Two-component regulatory system / DNA BINDING PROTEIN
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
: / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...: / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulatory protein WalR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsZhao, H. / Tang, L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Preliminary crystallographic studies of the regulatory domain of response regulator YycF from an essential two-component signal transduction system.
Authors: Zhao, H. / Heroux, A. / Sequeira, R.D. / Tang, L.
History
DepositionNov 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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
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: Transcriptional regulatory protein yycF


Theoretical massNumber of molelcules
Total (without water)13,7881
Polymers13,7881
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.495, 59.495, 79.059
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Transcriptional regulatory protein yycF


Mass: 13787.979 Da / Num. of mol.: 1 / Fragment: receiver domain of YycF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: Strain 168 / Gene: BSU40410, yycF / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37478
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M Ammonium sulfate and 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 11994 / % possible obs: 97.7 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.077 / Χ2: 2.702
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.469 / Num. unique all: 1151 / Χ2: 1.301 / % possible all: 95

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.495 / Cor.coef. Fo:Fc: 0.411 / Cor.coef. Io to Ic: 0.439
Highest resolutionLowest resolution
Rotation3 Å12 Å
Translation3 Å8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NXP

1nxp


Resolution: 1.95→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.832 / Cross valid method: THROUGHOUT / σ(F): 452
RfactorNum. reflection% reflectionSelection details
Rfree0.276 563 4.6 %Random
Rwork0.239 ---
obs-11041 90.2 %-
Solvent computationBsol: 59.71 Å2
Displacement parametersBiso max: 85.68 Å2 / Biso mean: 43.253 Å2 / Biso min: 21.21 Å2
Baniso -1Baniso -2Baniso -3
1-5.481 Å20 Å20 Å2
2--5.481 Å20 Å2
3----10.962 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 0 29 988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it3.5121.5
X-RAY DIFFRACTIONc_scbond_it4.7592
X-RAY DIFFRACTIONc_mcangle_it4.7252
X-RAY DIFFRACTIONc_scangle_it6.2782.5
LS refinement shellResolution: 1.95→2.02 Å
RfactorNum. reflection% reflection
Rfree0.2782 36 -
Rwork0.26 --
obs-686 95.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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