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- PDB-2gx5: N-terminal GAF domain of transcriptional pleiotropic repressor CodY -

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Basic information

Entry
Database: PDB / ID: 2gx5
TitleN-terminal GAF domain of transcriptional pleiotropic repressor CodY
ComponentsGTP-sensing transcriptional pleiotropic repressor codY
KeywordsTRANSCRIPTION / CodY / DNA-binding / Nucleotide-binding / Repressor / Transcription regulation / GAF domain / Branched chain amino acid binding
Function / homology
Function and homology information


DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / GTP 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 domain / GAF-like domain superfamily / Beta-Lactamase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...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 domain / GAF-like domain superfamily / Beta-Lactamase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CYCLIC GUANOSINE MONOPHOSPHATE / TRIETHYLENE GLYCOL / Global transcriptional regulator CodY
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsWilkinson, A.J. / Levdikov, V.M. / Blagova, E.V.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in gram-positive bacteria.
Authors: Levdikov, V.M. / Blagova, E. / Joseph, P. / Sonenshein, A.L. / Wilkinson, A.J.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: The Structure of CodY, a GTP- and Isoleucine-responsive Regulator of Stationary Phase and Virulence in Gram-positive Bacteria
Authors: Levdikov, V.M. / Blagova, E. / Joseph, P. / Sonenshein, A.L. / Wilkinson, A.J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization of the GTP-dependent transcriptional regulator CodY from Bacillus subtilis
Authors: Blagova, E.V. / Levdikov, V.M. / Tachikawa, K. / Sonenshein, A.L. / Wilkinson, A.J.
History
DepositionMay 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,94127
Polymers77,1884
Non-polymers2,75323
Water6,990388
1
A: GTP-sensing transcriptional pleiotropic repressor codY
B: GTP-sensing transcriptional pleiotropic repressor codY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3089
Polymers38,5942
Non-polymers7157
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-64 kcal/mol
Surface area15070 Å2
MethodPISA
2
C: GTP-sensing transcriptional pleiotropic repressor codY
D: GTP-sensing transcriptional pleiotropic repressor codY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,63318
Polymers38,5942
Non-polymers2,03916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-58 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.207, 90.207, 205.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
GTP-sensing transcriptional pleiotropic repressor codY / Vegetative protein 286B / VEG286B


Mass: 19296.902 Da / Num. of mol.: 4 / Fragment: N-terminal domain, residues 1-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: codY / Plasmid: pET-YSBLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P39779

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Non-polymers , 7 types, 411 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE


Mass: 345.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O7P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulphate, sodium citrate, PEG 400, 20mM cGMP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9757 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2005
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9757 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. all: 85808 / Num. obs: 85808 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.11
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.67 / Num. unique all: 8202 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B18

2b18


Resolution: 1.74→31.89 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.518 / SU ML: 0.067 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.161 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21595 4191 5 %RANDOM
Rwork0.18726 ---
all0.18872 79437 --
obs0.18872 79437 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.74→31.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 171 388 5598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225648
X-RAY DIFFRACTIONr_bond_other_d0.0010.023880
X-RAY DIFFRACTIONr_angle_refined_deg1.0761.9937610
X-RAY DIFFRACTIONr_angle_other_deg0.85539515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4125701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99225.267281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72151049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1151540
X-RAY DIFFRACTIONr_chiral_restr0.070.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021058
X-RAY DIFFRACTIONr_nbd_refined0.2080.21107
X-RAY DIFFRACTIONr_nbd_other0.1840.24031
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22621
X-RAY DIFFRACTIONr_nbtor_other0.0860.22877
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0260.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.62253735
X-RAY DIFFRACTIONr_mcbond_other1.09251375
X-RAY DIFFRACTIONr_mcangle_it3.41665501
X-RAY DIFFRACTIONr_scbond_it3.87982380
X-RAY DIFFRACTIONr_scangle_it5.221102096
X-RAY DIFFRACTIONr_rigid_bond_restr3.407310505
X-RAY DIFFRACTIONr_sphericity_free3.0973388
X-RAY DIFFRACTIONr_sphericity_bonded2.2139463
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 248 -
Rwork0.279 4844 -
obs-4191 89.6 %

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