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- PDB-2b18: N-terminal GAF domain of transcriptional pleiotropic repressor CodY. -

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Basic information

Entry
Database: PDB / ID: 2b18
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
ISOLEUCINE / Global transcriptional regulator CodY
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLevdikov, V.M. / Blagova, E. / Joseph, P. / Sonenshein, A.L. / Wilkinson, A.J.
CitationJournal: 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.
History
DepositionSep 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: GTP-sensing transcriptional pleiotropic repressor codY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6812
Polymers18,5501
Non-polymers1311
Water2,324129
1
A: GTP-sensing transcriptional pleiotropic repressor codY
hetero molecules

A: GTP-sensing transcriptional pleiotropic repressor codY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3624
Polymers37,1002
Non-polymers2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Unit cell
Length a, b, c (Å)34.696, 86.081, 54.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 18550.025 Da / Num. of mol.: 1 / Fragment: N-terminal domain
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
#2: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.2 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 5000, calcium acetate, isoleucine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 11, 2005 / Details: Rh coated collimating mirrors
RadiationMonochromator: Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 16841 / Num. obs: 16841 / % possible obs: 88.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.7 / Num. unique all: 275 / % possible all: 29.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.956 / SU ML: 0.084 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.224 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21234 775 5 %RANDOM
Rwork0.15351 ---
all0.1564 14653 --
obs0.1564 14653 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.063 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 9 129 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221275
X-RAY DIFFRACTIONr_bond_other_d0.0010.021192
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9841725
X-RAY DIFFRACTIONr_angle_other_deg0.80732776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17825.23863
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70415240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.726159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021421
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02244
X-RAY DIFFRACTIONr_nbd_refined0.2180.2262
X-RAY DIFFRACTIONr_nbd_other0.1810.21252
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2632
X-RAY DIFFRACTIONr_nbtor_other0.0830.2803
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0260.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.42641030
X-RAY DIFFRACTIONr_mcbond_other2.4334325
X-RAY DIFFRACTIONr_mcangle_it5.36261277
X-RAY DIFFRACTIONr_scbond_it7.6438547
X-RAY DIFFRACTIONr_scangle_it9.85410446
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 64 -
Rwork0.151 819 -
obs-819 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1167-0.22360.11741.52060.05280.18870.0542-0.04550.0079-0.1466-0.11740.1559-0.0086-0.07520.0631-0.02270.0088-0.01240.0068-0.02670.032228.69974.599215.1559
20.2999-0.3606-0.1260.9470.270.52780.07710.08860.0998-0.0888-0.1019-0.0082-0.0395-0.02980.0249-0.01960.01850.00190.01170.02610.006431.637222.006914.9374
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3610 - 45
2X-RAY DIFFRACTION1AA135 - 155144 - 164
3X-RAY DIFFRACTION2AA39 - 13348 - 142

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