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

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Basic information

Entry
Database: PDB / ID: 2hgv
TitleN-terminal GAF domain of transcriptional pleiotropic repressor CodY
ComponentsGTP-sensing transcriptional pleiotropic repressor codY
KeywordsDNA BINDING PROTEIN / 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
VALINE / Global transcriptional regulator CodY
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: 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
DepositionJun 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)18,9492
Polymers18,8311
Non-polymers1171
Water2,360131
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)37,8974
Polymers37,6632
Non-polymers2342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Unit cell
Length a, b, c (Å)34.690, 84.846, 54.929
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
11A-327-

HOH

21A-328-

HOH

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Components

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


Mass: 18831.396 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 1-154
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-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 5000, calcium acetate, valine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2005
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 7646 / Num. obs: 7646 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.361 / Num. unique all: 672 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B18

2b18


Resolution: 2.3→27.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.285 / SU ML: 0.158 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24418 350 4.6 %RANDOM
Rwork0.16427 ---
all0.16804 7231 --
obs0.16804 7231 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: 39.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 8 131 1375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221260
X-RAY DIFFRACTIONr_bond_other_d0.0010.021182
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9851703
X-RAY DIFFRACTIONr_angle_other_deg0.81932752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.525.32362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73515238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.204159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02238
X-RAY DIFFRACTIONr_nbd_refined0.2090.2265
X-RAY DIFFRACTIONr_nbd_other0.1960.21209
X-RAY DIFFRACTIONr_nbtor_refined0.170.2623
X-RAY DIFFRACTIONr_nbtor_other0.0870.2706
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.834965
X-RAY DIFFRACTIONr_mcbond_other0.8584323
X-RAY DIFFRACTIONr_mcangle_it3.70161266
X-RAY DIFFRACTIONr_scbond_it3.7388524
X-RAY DIFFRACTIONr_scangle_it5.36710435
X-RAY DIFFRACTIONr_rigid_bond_restr1.67732786
X-RAY DIFFRACTIONr_sphericity_free4.2563131
X-RAY DIFFRACTIONr_sphericity_bonded1.90132426
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 14 -
Rwork0.168 479 -
obs-479 100 %

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