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- PDB-8c7t: Unliganded transcriptional pleiotropic repressor CodY from Entero... -

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Basic information

Entry
Database: PDB / ID: 8c7t
TitleUnliganded transcriptional pleiotropic repressor CodY from Enterococcus faecalis
ComponentsGTP-sensing transcriptional pleiotropic repressor CodY
KeywordsTRANSCRIPTION / LEUCINE BINDING / PLEIOTROPIC TRANSCRIPTION / REGULATOR
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
Global transcriptional regulator CodY
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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

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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


Theoretical massNumber of molelcules
Total (without water)116,3334
Polymers116,3334
Non-polymers00
Water2,540141
1
A: GTP-sensing transcriptional pleiotropic repressor CodY
B: GTP-sensing transcriptional pleiotropic repressor CodY


Theoretical massNumber of molelcules
Total (without water)58,1672
Polymers58,1672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-39 kcal/mol
Surface area27640 Å2
MethodPISA
2
C: GTP-sensing transcriptional pleiotropic repressor CodY
D: GTP-sensing transcriptional pleiotropic repressor CodY


Theoretical massNumber of molelcules
Total (without water)58,1672
Polymers58,1672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-40 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.988, 171.241, 215.236
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Protein, 600 microM in 20 mM TrisCl pH 8, 450 mM NaCl Well, 200 mM ammoniumhydrogenphosphate, 2.5% EtOH, 23-25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.21→35.87 Å / Num. obs: 62752 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.995 / Rpim(I) all: 0.077 / Net I/σ(I): 7.3
Reflection shellResolution: 2.21→2.29 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6079 / CC1/2: 0.501 / Rpim(I) all: 0.876

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→35.87 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2734 3188 5.08 %
Rwork0.2357 --
obs0.2376 62734 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7511 0 0 141 7652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147617
X-RAY DIFFRACTIONf_angle_d1.29110286
X-RAY DIFFRACTIONf_dihedral_angle_d22.3852870
X-RAY DIFFRACTIONf_chiral_restr0.0591217
X-RAY DIFFRACTIONf_plane_restr0.0081315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.240.37031370.34282465X-RAY DIFFRACTION100
2.24-2.280.39731530.33122507X-RAY DIFFRACTION100
2.28-2.320.36011410.31292562X-RAY DIFFRACTION100
2.32-2.360.2931290.30342640X-RAY DIFFRACTION100
2.36-2.40.32061190.30842486X-RAY DIFFRACTION100
2.4-2.440.36481160.30752539X-RAY DIFFRACTION100
2.44-2.490.33641290.28612589X-RAY DIFFRACTION100
2.49-2.550.34271510.28642606X-RAY DIFFRACTION100
2.55-2.610.31971480.26332466X-RAY DIFFRACTION100
2.61-2.670.31551330.26112563X-RAY DIFFRACTION100
2.67-2.740.33761420.26412635X-RAY DIFFRACTION100
2.75-2.830.28711350.27332516X-RAY DIFFRACTION100
2.83-2.920.31931370.28152581X-RAY DIFFRACTION100
2.92-3.020.3481510.28432600X-RAY DIFFRACTION100
3.02-3.140.27231320.26362537X-RAY DIFFRACTION100
3.14-3.280.32981390.25152649X-RAY DIFFRACTION100
3.28-3.460.26271140.24282574X-RAY DIFFRACTION100
3.46-3.670.2651480.22312652X-RAY DIFFRACTION100
3.67-3.960.26761450.22452560X-RAY DIFFRACTION100
3.96-4.360.22771180.19492656X-RAY DIFFRACTION100
4.36-4.980.18881430.17842646X-RAY DIFFRACTION100
4.98-6.270.23991570.2122703X-RAY DIFFRACTION100
6.27-35.870.23851710.1952814X-RAY DIFFRACTION98

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