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- PDB-5n0l: The structure of the cofactor binding GAF domain of the nutrient ... -

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Basic information

Entry
Database: PDB / ID: 5n0l
TitleThe structure of the cofactor binding GAF domain of the nutrient sensor CodY from Clostridium difficile
ComponentsGTP-sensing transcriptional pleiotropic repressor CodY
KeywordsTRANSCRIPTION / Nutrient sensor / transcription regulation / GAF domain / clostridium
Function / homology
Function and homology information


DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / GTP binding / DNA binding / cytoplasm
Similarity search - Function
GTP-sensing transcriptional pleiotropic repressor CodY, N-terminal / GTP-sensing helix-turn-helix, CodY, C-terminal / GTP-sensing transcriptional pleiotropic repressor CodY / CodY GAF-like domain / CodY helix-turn-helix domain / GAF-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ISOLEUCINE / Global transcriptional regulator CodY / Global transcriptional regulator CodY
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLevdikov, V.M. / Blagova, E.V. / Wilkinson, A.J. / Sonenshein, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of HealthGM042219 United States
Citation
Journal: Plos One / Year: 2019
Title: Impact of CodY protein on metabolism, sporulation and virulence in Clostridioides difficile ribotype 027.
Authors: Daou, N. / Wang, Y. / Levdikov, V.M. / Nandakumar, M. / Livny, J. / Bouillaut, L. / Blagova, E. / Zhang, K. / Belitsky, B.R. / Rhee, K. / Wilkinson, A.J. / Sun, X. / Sonenshein, A.L.
#1: Journal: J. Biol. Chem. / Year: 2017
Title: Structure of the Branched-chain Amino Acid and GTP-sensing Global Regulator, CodY, from Bacillus subtilis.
Authors: Levdikov, V.M. / Blagova, E. / Young, V.L. / Belitsky, B.R. / Lebedev, A. / Sonenshein, A.L. / Wilkinson, A.J.
History
DepositionFeb 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 2.0Nov 21, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / struct_conn / Item: _atom_site.occupancy
Revision 2.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: GTP-sensing transcriptional pleiotropic repressor CodY
B: GTP-sensing transcriptional pleiotropic repressor CodY
C: GTP-sensing transcriptional pleiotropic repressor CodY
D: GTP-sensing transcriptional pleiotropic repressor CodY
E: GTP-sensing transcriptional pleiotropic repressor CodY
F: GTP-sensing transcriptional pleiotropic repressor CodY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,92012
Polymers104,1336
Non-polymers7876
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-101 kcal/mol
Surface area39650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.890, 190.390, 43.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-380-

HOH

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Components

#1: Protein
GTP-sensing transcriptional pleiotropic repressor CodY


Mass: 17355.488 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: codY, BN1095_790003, BN1096_560190, BN1097_540194 / Plasmid: pET-YSBLIC-3C / Details (production host): encodes cleavage his tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A031WD25, UniProt: Q18BE1*PLUS
#2: Chemical
ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 48.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% polyethylene glycol 3350, 0.2 M sodium formate, 0.1 M Bis-tris-propane, pH 6.5 and protein solutions containing 10 mM isoleucine.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.68→56.19 Å / Num. obs: 115569 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.1
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.81 / Num. unique obs: 8396 / CC1/2: 0.515 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B18

2b18


Resolution: 1.68→56.19 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.953 / SU B: 8.491 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 5726 5 %RANDOM
Rwork0.15406 ---
obs0.15778 109833 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.644 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0 Å2
2---0.39 Å20 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.68→56.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7230 0 54 648 7932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0197619
X-RAY DIFFRACTIONr_bond_other_d0.0030.027213
X-RAY DIFFRACTIONr_angle_refined_deg2.5381.98810312
X-RAY DIFFRACTIONr_angle_other_deg1.319316826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6835990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.48926.296324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.788151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4151524
X-RAY DIFFRACTIONr_chiral_restr0.1510.21247
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028466
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021350
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_it6.3093.3923924
X-RAY DIFFRACTIONr_mcbond_other6.313.3923923
X-RAY DIFFRACTIONr_mcangle_it7.5915.1024890
X-RAY DIFFRACTIONr_mcangle_other7.595.1014891
X-RAY DIFFRACTIONr_scbond_it7.7234.083695
X-RAY DIFFRACTIONr_scbond_other7.7234.083695
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6955.865411
X-RAY DIFFRACTIONr_long_range_B_refined8.69441.6058215
X-RAY DIFFRACTIONr_long_range_B_other8.65241.3378127
X-RAY DIFFRACTIONr_rigid_bond_restr5.349314829
X-RAY DIFFRACTIONr_sphericity_free35.6215440
X-RAY DIFFRACTIONr_sphericity_bonded25.944514953
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 408 -
Rwork0.287 7981 -
obs--99.94 %

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