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- PDB-6ebb: Crystal Structure of YycF homologue, crystals grown in Tris buffer -

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Basic information

Entry
Database: PDB / ID: 6ebb
TitleCrystal Structure of YycF homologue, crystals grown in Tris buffer
ComponentsDNA-binding response regulator
KeywordsSIGNALING PROTEIN / YycF / Essential / Response Regulator / Receiver Domain
Function / homology
Function and homology information


phosphorelay signal transduction system / cis-regulatory region sequence-specific DNA binding / fatty acid biosynthetic process / negative regulation of DNA-templated transcription / membrane / cytosol
Similarity search - Function
: / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / 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 / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / 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 speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.022 Å
AuthorsRiboldi-Tunnicliffe, A. / Panjikar, S. / Williamson, R.M. / Gabrielsen, M.
CitationJournal: To Be Published
Title: Crystal Structure of YycF homologue, crystals grown in Tris buffer
Authors: Riboldi-Tunnicliffe, A. / Panjikar, S.
History
DepositionAug 6, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionAug 14, 2019ID: 2A9Q
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)13,6011
Polymers13,6011
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.563, 93.324, 37.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

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Components

#1: Protein DNA-binding response regulator / YycF homologue


Mass: 13600.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1227 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UQ68
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 30% (vol/vol) polyethylene glycol 300 (PEG-300), 0.1 M Tris-HCl buffer (pH 7.0)
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 4, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→31.51 Å / Num. obs: 6892 / % possible obs: 93.77 % / Redundancy: 2 % / Biso Wilson estimate: 36.42 Å2 / Net I/σ(I): 2
Reflection shellResolution: 2→2.25 Å / Num. unique obs: 682 / % possible all: 95.09

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NXT

1nxt


Resolution: 2.022→31.505 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.9
RfactorNum. reflection% reflection
Rfree0.255 328 4.76 %
Rwork0.2113 --
obs0.2134 6892 77.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.022→31.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 0 31 953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014933
X-RAY DIFFRACTIONf_angle_d1.6431255
X-RAY DIFFRACTIONf_dihedral_angle_d30.512364
X-RAY DIFFRACTIONf_chiral_restr0.109147
X-RAY DIFFRACTIONf_plane_restr0.017162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.022-2.54730.35611290.2952536X-RAY DIFFRACTION61
2.5473-31.50930.2321990.1944028X-RAY DIFFRACTION93

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