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- PDB-3ly8: Crystal structure of mutant D471E of the periplasmic domain of CadC -

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Basic information

Entry
Database: PDB / ID: 3ly8
TitleCrystal structure of mutant D471E of the periplasmic domain of CadC
ComponentsTranscriptional activator cadC
KeywordsSIGNALING PROTEIN / alpha/beta domain / alpha domain / Activator / DNA-binding / Membrane / Transcription regulation / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / plasma membrane / cytosol
Similarity search - Function
Rossmann fold - #11830 / CadC C-terminal domain 1 / CadC C-terminal domain 1 / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Signal transduction response regulator, C-terminal effector / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Rossmann fold - #11830 / CadC C-terminal domain 1 / CadC C-terminal domain 1 / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Signal transduction response regulator, C-terminal effector / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcriptional activator CadC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEichinger, A. / Skerra, A.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystal structure of the sensory domain of Escherichia coli CadC, a member of the ToxR-like protein family.
Authors: Eichinger, A. / Haneburger, I. / Koller, C. / Jung, K. / Skerra, A.
History
DepositionFeb 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional activator cadC


Theoretical massNumber of molelcules
Total (without water)41,9101
Polymers41,9101
Non-polymers00
Water4,216234
1
A: Transcriptional activator cadC

A: Transcriptional activator cadC


Theoretical massNumber of molelcules
Total (without water)83,8202
Polymers83,8202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area3980 Å2
ΔGint-12 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.630, 83.630, 199.491
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-48-

HOH

21A-517-

HOH

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Components

#1: Protein Transcriptional activator cadC


Mass: 41910.086 Da / Num. of mol.: 1 / Fragment: residues 188-512 / Mutation: D471E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MG1655 / Gene: b4133, cadC, JW4094 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) pLysS / References: UniProt: P23890
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7 M ammonium sulfate, 5% (v/v) 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 30, 2009 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.897→72.43 Å / Num. all: 33613 / Num. obs: 33613 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Rsym value: 0.086
Reflection shellResolution: 1.9→2 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 8.8 / Num. unique all: 4789 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LY7

3ly7


Resolution: 1.9→72.43 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.867 / SU B: 2.713 / SU ML: 0.082 / SU R Cruickshank DPI: 0.143 / SU Rfree: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1697 5.1 %RANDOM
Rwork0.202 ---
all0.203 ---
obs0.203 33530 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.42 Å2 / Biso mean: 22.376 Å2 / Biso min: 9.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→72.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 0 234 2800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222617
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9593554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9215322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60925.242124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82815459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3851512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211971
X-RAY DIFFRACTIONr_mcbond_it0.8831.51612
X-RAY DIFFRACTIONr_mcangle_it1.61622607
X-RAY DIFFRACTIONr_scbond_it2.44831005
X-RAY DIFFRACTIONr_scangle_it3.9674.5947
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 118 -
Rwork0.229 2306 -
all-2424 -
obs-2306 100 %

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