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- PDB-3lya: Crystal structure of the periplasmic domain of CadC in the presen... -

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Basic information

Entry
Database: PDB / ID: 3lya
TitleCrystal structure of the periplasmic domain of CadC in the presence of K2ReCl6
ComponentsTranscriptional activator cadC
KeywordsSIGNALING PROTEIN / alpha/beta domain / alpha domain / Activator / DNA-binding / Transcription regulation / 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 / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / 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 / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / 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
rhenium (IV) hexachloride / Transcriptional activator CadC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional activator cadC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,27917
Polymers41,8961
Non-polymers6,38316
Water61334
1
A: Transcriptional activator cadC
hetero molecules

A: Transcriptional activator cadC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,55834
Polymers83,7922
Non-polymers12,76632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area2900 Å2
ΔGint-13 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.561, 80.561, 199.783
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-5-

RHE

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Components

#1: Protein Transcriptional activator cadC


Mass: 41896.059 Da / Num. of mol.: 1 / Fragment: residues 188-512
Source method: isolated from a genetically manipulated source
Details: The plasmid encodes a fusion protein comprising bacterial thioredoxin, a double His6-tag interspersed with a thrombin and an enterokinase cleavage site, and the CadC fragment comprising ...Details: The plasmid encodes a fusion protein comprising bacterial thioredoxin, a double His6-tag interspersed with a thrombin and an enterokinase cleavage site, and the CadC fragment comprising residues 188-512. Amino acid numbering of the crystal structure corresponds to the original numbering of the full length CadC protein sequence.
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: Chemical
ChemComp-RHE / rhenium (IV) hexachloride / hexachlororhenate ion


Mass: 398.925 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl6Re
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M ammonium sulfate, 6 % (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: 1.17652, 1.17705, 1.07813
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 2008 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.176521
21.177051
31.078131
ReflectionRedundancy: 14.1 % / Av σ(I) over netI: 6.2 / Number: 247813 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / D res high: 2.3 Å / D res low: 69.768 Å / Num. obs: 17592 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.2739.4998.310.0460.04611.7
5.147.2799.910.0570.05713.2
4.25.1499.610.0690.06913.7
3.644.299.610.0830.08313.9
3.253.6499.310.0830.08314.2
2.973.2599.110.1060.10614.2
2.752.9799.110.1370.13714.3
2.572.7598.810.1950.19514.4
2.422.5798.610.2610.26114.4
2.32.4298.410.3550.35514.5
ReflectionResolution: 2.3→69.77 Å / Num. all: 17592 / Num. obs: 17592 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Rsym value: 0.095 / Net I/σ(I): 19.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 7.3 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MAD / Resolution: 2.3→69.77 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.854 / Occupancy max: 1 / Occupancy min: 0 / SU B: 6.257 / SU ML: 0.157 / SU R Cruickshank DPI: 0.357 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27134 897 5.1 %RANDOM
Rwork0.22984 ---
obs0.2319 16693 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→69.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 112 34 2674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222675
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7522.0263745
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37525.366123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15315449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7611511
X-RAY DIFFRACTIONr_chiral_restr0.10.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211946
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8851.51587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59822568
X-RAY DIFFRACTIONr_scbond_it3.16731088
X-RAY DIFFRACTIONr_scangle_it3.8884.51177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 71 -
Rwork0.253 1170 -
obs--97.87 %

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