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- PDB-8c7o: Unliganded transcriptional pleiotropic repressor CodY from Staphy... -

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Basic information

Entry
Database: PDB / ID: 8c7o
TitleUnliganded transcriptional pleiotropic repressor CodY from Staphylococcus aureus
ComponentsGlobal transcriptional regulator CodY
KeywordsTRANSCRIPTION / GTP SENSING / 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 / GAF-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / Global transcriptional regulator CodY
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 16, 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: Global transcriptional regulator CodY
B: Global transcriptional regulator CodY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,63721
Polymers57,8492
Non-polymers1,78819
Water1,76598
1
A: Global transcriptional regulator CodY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6569
Polymers28,9241
Non-polymers7318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Global transcriptional regulator CodY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,98112
Polymers28,9241
Non-polymers1,05711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.803, 163.852, 46.868
Angle α, β, γ (deg.)90.00, 93.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Global transcriptional regulator CodY


Mass: 28924.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Gene: codY, SAHV_1245 / Production host: Escherichia coli (E. coli) / References: UniProt: A7X1N2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein, 270 microM in 20 mM Tris-Cl pH 8, 200 mM NaCl, 1 mM DTT Well, 200 mM ammoniumsulphate, 100 mM NaAc pH4.6, 22-25% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.05→46.76 Å / Num. obs: 33429 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 37.5 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.074 / Net I/σ(I): 5.6
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3376 / CC1/2: 0.44 / Rpim(I) all: 0.799 / % possible all: 100

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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: 2.05→45 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.256 -5 %
Rwork0.213 --
obs-33428 99.4 %
Refinement stepCycle: LAST / Resolution: 2.05→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 94 98 4210
LS refinement shellResolution: 2.05→2.12 Å
RfactorNum. reflection% reflection
Rfree0.406 --
Rwork0.343 3376 -
obs--100 %

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