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Basic information

Entry
Database: PDB / ID: 5loe
TitleStructure of full length Cody from Bacillus subtilis in complex with Ile
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
ISOLEUCINE / Global transcriptional regulator CodY
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,7308
Polymers117,2064
Non-polymers5254
Water1629
1
A: GTP-sensing transcriptional pleiotropic repressor CodY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4332
Polymers29,3011
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-sensing transcriptional pleiotropic repressor CodY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4332
Polymers29,3011
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTP-sensing transcriptional pleiotropic repressor CodY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4332
Polymers29,3011
Non-polymers1311
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTP-sensing transcriptional pleiotropic repressor CodY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4332
Polymers29,3011
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.690, 158.877, 55.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13A
23B
14C
24D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 179
2114B1 - 179
1124C1 - 179
2124D1 - 179
1134A180 - 258
2134B180 - 258
1144C180 - 258
2144D180 - 258

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.089363, -0.927042, 0.364153), (-0.929854, -0.053364, -0.364038), (0.356911, -0.371141, -0.857245)-7.47884, -7.50021, 0.18809
3given(-0.088483, -0.924447, 0.370903), (-0.932078, -0.054477, -0.358137), (0.351284, -0.377399, -0.856837)-7.36435, -7.57515, 0.2153
4given(-0.109301, -0.895266, 0.431917), (-0.882774, -0.112304, -0.456177), (0.456905, -0.431146, -0.778043)-6.18354, -9.39646, -1.76055
5given(-0.094894, -0.937743, 0.334115), (-0.94213, -0.023808, -0.334401), (0.321537, -0.346512, -0.881217)-7.48453, -6.97025, 2.336

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Components

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


Mass: 29301.377 Da / Num. of mol.: 4 / Mutation: L3S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: codY, BSU16170 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P39779
#2: Chemical
ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG5000, 0.1M HEPES pH 7.5, 5% tacsimate, 20mM Ile

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 22830 / % possible obs: 92.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 0.96 / % possible all: 47.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B18, 2B0L

2b18

2b0l


Resolution: 3→45.45 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.892 / SU B: 65.422 / SU ML: 0.505 / Cross valid method: THROUGHOUT / ESU R Free: 0.582 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30162 1164 5.1 %RANDOM
Rwork0.21225 ---
obs0.21693 21606 92.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 110.383 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--2.04 Å2-0 Å2
3----1.38 Å2
Refinement stepCycle: 1 / Resolution: 3→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8068 0 36 9 8113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198258
X-RAY DIFFRACTIONr_bond_other_d0.0020.028217
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.98511129
X-RAY DIFFRACTIONr_angle_other_deg1.078318908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88151049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21825.255392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.774151617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2541561
X-RAY DIFFRACTIONr_chiral_restr0.1080.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029353
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021764
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_it9.35915.6774151
X-RAY DIFFRACTIONr_mcbond_other9.34215.6694150
X-RAY DIFFRACTIONr_mcangle_it13.52626.3925182
X-RAY DIFFRACTIONr_mcangle_other13.52526.4055183
X-RAY DIFFRACTIONr_scbond_it10.93317.7694107
X-RAY DIFFRACTIONr_scbond_other10.91517.7694107
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.8929.0845937
X-RAY DIFFRACTIONr_long_range_B_refined20.48133792
X-RAY DIFFRACTIONr_long_range_B_other20.48233792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2814medium positional0.20.5
2C2816medium positional0.210.5
3A1216medium positional0.870.5
4C1242medium positional0.650.5
1A2814medium thermal8.32
2C2816medium thermal9.12
3A1216medium thermal9.752
4C1242medium thermal11.372
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.502 44 -
Rwork0.414 727 -
obs--42.48 %
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)
12.8742-0.3563-0.36034.7428-1.95754.96690.03430.27330.49570.21710.2541-0.0755-0.6577-0.3288-0.28850.3404-0.06250.090.20670.17470.41930.64810.622-9.243
26.6214-0.7920.23042.5946-0.11272.5607-0.33480.26220.0303-0.1259-0.21970.364-0.0277-0.27410.55450.3494-0.1237-0.01790.1351-0.17450.3965-23.662-32.64515.388
37.4151-0.89090.68413.16380.69454.6168-0.0926-0.2515-0.46640.33280.2971-0.7899-0.06220.033-0.20450.3114-0.0868-0.16110.1020.05090.593954.581-12.8573.72
45.9542-1.1240.56744.4151.69654.2794-0.4061-0.5048-1.96820.72450.0781-0.12490.6370.30740.32790.4810.04880.30130.09130.2691.1060.671-58.26421.87
517.65610.4192-11.44896.953-6.8418.19670.10070.7009-1.07470.7245-0.1373-0.9403-0.5991-0.64510.03650.8239-0.25170.12570.50610.35130.794323.579-7.5243.948
614.21887.911-9.17845.1264-5.23396.1005-0.03870.3056-0.69710.1653-0.2803-0.2563-0.076-0.02070.31890.537-0.08790.06560.4497-0.02540.3545-1.388-30.1218.09
714.462912.0042-2.098711.7293-1.00980.65330.02750.3818-0.22460.6920.2069-0.44120.2115-0.1409-0.23430.4802-0.03930.00380.2970.24160.694631.88-18.7652.021
818.660315.5774-0.992814.3319-0.95930.7490.08230.4228-0.50130.5614-0.1212-0.1449-0.03760.2560.03890.5152-0.05310.15210.3530.09380.59347.49-36.5217.107
93.1081-0.0418-0.23967.78670.31875.4037-0.0961-0.08170.5225-0.1127-0.35440.8198-0.1668-0.41590.45050.39780.0159-0.06090.3012-0.03490.3916-1.642-12.31221.587
101.9085-0.77071.66851.3174-1.972612.3636-0.05030.094-0.0619-0.0978-0.27230.0031-0.42560.1410.32260.4028-0.0793-0.01030.38930.07850.198512.785-13.866-14.901
117.98231.72774.79326.8620.97863.0227-0.20671.0444-1.5939-0.43770.8231-0.72090.09370.6281-0.61640.50880.0120.49670.3519-0.26031.138616.267-45.749-2.11
125.82880.183-1.50374.57652.05979.603-0.051-0.3447-0.08510.41430.0075-0.4385-0.22941.45570.04360.4131-0.0169-0.19330.68240.24470.320432.864-19.84724.78
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 138
2X-RAY DIFFRACTION2B2 - 138
3X-RAY DIFFRACTION3C2 - 138
4X-RAY DIFFRACTION4D2 - 138
5X-RAY DIFFRACTION5A139 - 179
6X-RAY DIFFRACTION6B139 - 179
7X-RAY DIFFRACTION7C139 - 179
8X-RAY DIFFRACTION8D139 - 179
9X-RAY DIFFRACTION9A180 - 258
10X-RAY DIFFRACTION10B180 - 258
11X-RAY DIFFRACTION11C180 - 258
12X-RAY DIFFRACTION12D180 - 258

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