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- PDB-5loj: Structure of full length unliganded CodY from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 5loj
TitleStructure of full length unliganded CodY from Bacillus subtilis
ComponentsGTP-sensing transcriptional pleiotropic repressor CodY
KeywordsTRANSCRIPTION / GAF / wHTH / transcriptional regulator / CodY
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-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Global transcriptional regulator CodY
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.71 Å
AuthorsWilkinson, A.J. / Levdikov, V.M. / Blagova, E.V.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBBS/B1213X United Kingdom
Wellcome Trust082829/Z/07/Z United Kingdom
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)GM042219 United States
Citation
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.
#1: Journal: J. Mol. Biol. / Year: 2009
Title: Structural rearrangement accompanying ligand binding in the GAF domain of CodY from Bacillus subtilis.
Authors: Levdikov, V.M. / Blagova, E. / Colledge, V.L. / Lebedev, A.A. / Williamson, D.C. / Sonenshein, A.L. / Wilkinson, A.J.
#2: 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.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 9, 2018Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.4Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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


Theoretical massNumber of molelcules
Total (without water)59,2092
Polymers59,2092
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.524, 111.524, 119.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 2 - 256 / Label seq-ID: 1 - 255

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.288335, -0.006144, -0.95751), (0.022567, -0.999745, -0.000381), (-0.957264, -0.021718, 0.2884)-71.99015, -41.45104, -54.30959

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Components

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


Mass: 29604.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: codY, BSU16170 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P39779

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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: 3.1 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 1.7M Li2SO4, sodium citrate pH 5.6, 3% dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.7→25 Å / Num. obs: 8235 / % possible obs: 97.5 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 33.14
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 5.66 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GX5, 2B0L

2gx5

2b0l


Resolution: 3.71→24.94 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.83 / SU B: 115.534 / SU ML: 0.82 / Cross valid method: THROUGHOUT / ESU R Free: 1.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.38942 381 4.6 %RANDOM
Rwork0.26356 ---
obs0.26905 7841 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 83.452 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å2-0 Å2
2--0.45 Å2-0 Å2
3----0.9 Å2
Refinement stepCycle: 1 / Resolution: 3.71→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4004 0 0 0 4004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194044
X-RAY DIFFRACTIONr_bond_other_d0.0020.024020
X-RAY DIFFRACTIONr_angle_refined_deg2.1351.9855446
X-RAY DIFFRACTIONr_angle_other_deg3.42139240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1725508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.50225.208192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.92815784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5821530
X-RAY DIFFRACTIONr_chiral_restr0.1340.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024570
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02864
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_it22.97410.9572038
X-RAY DIFFRACTIONr_mcbond_other22.94710.9562037
X-RAY DIFFRACTIONr_mcangle_it20.65624.6132544
X-RAY DIFFRACTIONr_mcangle_other20.65824.6122545
X-RAY DIFFRACTIONr_scbond_it23.67811.8722006
X-RAY DIFFRACTIONr_scbond_other23.67211.8682007
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other20.66726.0832903
X-RAY DIFFRACTIONr_long_range_B_refined20.78917124
X-RAY DIFFRACTIONr_long_range_B_other20.78917124
X-RAY DIFFRACTIONr_rigid_bond_restr77.22137989
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded40.89958024
Refine LS restraints NCS

Ens-ID: 1 / Number: 4012 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.690.5
1Amedium thermal24.462
2Bmedium positional0.690.5
2Bmedium thermal24.462
LS refinement shellResolution: 3.706→3.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 33 -
Rwork0.285 540 -
obs--95.5 %

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