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- PDB-8c7u: Transcriptional pleiotropic repressor CodY from Enterococcus faec... -

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Basic information

Entry
Database: PDB / ID: 8c7u
TitleTranscriptional pleiotropic repressor CodY from Enterococcus faecalis in complex with Leu and a 30-bp DNA fragment encompassing two overlapping binding sites
Components
  • DNA (29-MER)
  • DNA (30-MER)
  • GTP-sensing transcriptional pleiotropic repressor CodY
KeywordsTRANSCRIPTION / LEUCINE BINDING / PLEIOTROPIC TRANSCRIPTION / REGULATOR / DNA COMPLEX
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / GTP binding / DNA 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 / ArsR-like 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
LEUCINE / : / DNA / DNA (> 10) / Global transcriptional regulator CodY
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsHainzl, T. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural insights into CodY activation and DNA recognition.
Authors: Hainzl, T. / Bonde, M. / Almqvist, F. / Johansson, J. / Sauer-Eriksson, A.E.
History
DepositionJan 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 23, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 15, 2023Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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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: DNA (29-MER)
F: DNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0899
Polymers134,7716
Non-polymers3173
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.747, 98.692, 168.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
GTP-sensing transcriptional pleiotropic repressor CodY


Mass: 29083.346 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria)
Gene: codY, CGZ46_07460, CUM81_01520, DAI13_08275, EY666_04655, GTI81_07970, H9Q64_02750, JFI91_04250
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B4XP18
#2: DNA chain DNA (29-MER)


Mass: 9178.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#3: DNA chain DNA (30-MER)


Mass: 9259.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#4: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Protein,200 microM in 20 mM TrisCl pH 8, 150 mM NaCl,4 mM Leu, 60 microM DNA Well, 0.01 M CoCl2, 0.01 M MnCl2, 0.1 M NaAc pH 4.6,1 M 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9116 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 3.15→48.79 Å / Num. obs: 25663 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 112 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.073 / Net I/σ(I): 8.5
Reflection shellResolution: 3.15→3.26 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2516 / CC1/2: 0.441 / Rpim(I) all: 1.01

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Processing

Software
NameVersionClassification
PHENIXphenix1.17.1refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→48.79 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2847 1260 4.91 %
Rwork0.248 --
obs0.2498 25663 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8097 1211 19 0 9327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049572
X-RAY DIFFRACTIONf_angle_d0.76213175
X-RAY DIFFRACTIONf_dihedral_angle_d19.3983688
X-RAY DIFFRACTIONf_chiral_restr0.0441551
X-RAY DIFFRACTIONf_plane_restr0.0041474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.280.41461090.38412691X-RAY DIFFRACTION100
3.28-3.430.36581450.32852650X-RAY DIFFRACTION100
3.43-3.610.35691570.30092657X-RAY DIFFRACTION100
3.61-3.830.30831430.29392680X-RAY DIFFRACTION100
3.83-4.130.36051390.2772690X-RAY DIFFRACTION100
4.13-4.540.26391460.24492694X-RAY DIFFRACTION100
4.54-5.20.28341430.24392698X-RAY DIFFRACTION100
5.2-6.550.34581350.26762770X-RAY DIFFRACTION100
6.55-48.790.21291430.19532873X-RAY DIFFRACTION100

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