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

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Basic information

Entry
Database: PDB / ID: 5loo
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: 4.5 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 1.3Nov 21, 2018Group: Data collection / Derived calculations / Category: struct_conn
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 / pdbx_initial_refinement_model

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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
G: GTP-sensing transcriptional pleiotropic repressor CodY
H: GTP-sensing transcriptional pleiotropic repressor CodY
I: GTP-sensing transcriptional pleiotropic repressor CodY
J: GTP-sensing transcriptional pleiotropic repressor CodY
K: GTP-sensing transcriptional pleiotropic repressor CodY
L: GTP-sensing transcriptional pleiotropic repressor CodY
M: GTP-sensing transcriptional pleiotropic repressor CodY
N: GTP-sensing transcriptional pleiotropic repressor CodY


Theoretical massNumber of molelcules
Total (without water)414,46614
Polymers414,46614
Non-polymers00
Water00
1
M: GTP-sensing transcriptional pleiotropic repressor CodY

N: GTP-sensing transcriptional pleiotropic repressor CodY


Theoretical massNumber of molelcules
Total (without water)59,2092
Polymers59,2092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
2
N: GTP-sensing transcriptional pleiotropic repressor CodY

M: GTP-sensing transcriptional pleiotropic repressor CodY


Theoretical massNumber of molelcules
Total (without water)59,2092
Polymers59,2092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
3
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-16 kcal/mol
Surface area27970 Å2
MethodPISA
4
C: GTP-sensing transcriptional pleiotropic repressor CodY
D: GTP-sensing transcriptional pleiotropic repressor CodY


Theoretical massNumber of molelcules
Total (without water)59,2092
Polymers59,2092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-14 kcal/mol
Surface area28390 Å2
MethodPISA
5
E: GTP-sensing transcriptional pleiotropic repressor CodY
F: GTP-sensing transcriptional pleiotropic repressor CodY


Theoretical massNumber of molelcules
Total (without water)59,2092
Polymers59,2092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-15 kcal/mol
Surface area28130 Å2
MethodPISA
6
G: GTP-sensing transcriptional pleiotropic repressor CodY
H: GTP-sensing transcriptional pleiotropic repressor CodY


Theoretical massNumber of molelcules
Total (without water)59,2092
Polymers59,2092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-15 kcal/mol
Surface area28000 Å2
MethodPISA
7
I: GTP-sensing transcriptional pleiotropic repressor CodY
J: GTP-sensing transcriptional pleiotropic repressor CodY


Theoretical massNumber of molelcules
Total (without water)59,2092
Polymers59,2092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-13 kcal/mol
Surface area27910 Å2
MethodPISA
8
K: GTP-sensing transcriptional pleiotropic repressor CodY
L: GTP-sensing transcriptional pleiotropic repressor CodY


Theoretical massNumber of molelcules
Total (without water)59,2092
Polymers59,2092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-15 kcal/mol
Surface area28820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)315.628, 113.676, 168.594
Angle α, β, γ (deg.)90.00, 113.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 29604.713 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: codY, BSU16170 / Production host: Escherichia coli BL21 (bacteria) / 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: 3.4 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1M sodium citrate pH6.0, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.9804 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 4.5→20 Å / Num. obs: 29671 / % possible obs: 71.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.77
Reflection shellResolution: 4.5→4.58 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.01 / % possible all: 71.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LOJ

5loj


Resolution: 4.5→19.88 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.824 / SU B: 165.968 / SU ML: 2.029 / Cross valid method: THROUGHOUT / ESU R Free: 1.999 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.42963 1479 5.1 %RANDOM
Rwork0.25054 ---
obs0.26008 27647 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 235.091 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å211.4 Å2
2--8.16 Å20 Å2
3---2.83 Å2
Refinement stepCycle: 1 / Resolution: 4.5→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28154 0 0 0 28154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02228854
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.98138850
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.20253626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.59825.2581358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.427155586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.07915196
X-RAY DIFFRACTIONr_chiral_restr0.0920.24550
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0221210
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.216056
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.218772
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.21200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.2274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.071618728
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.629729064
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.707911313
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.361119786
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.5→4.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 113 -
Rwork0.357 1922 -
obs--100 %

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