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- PDB-5ey1: Crystal structure of CodY from Staphylococcus aureus with GTP and Ile -

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Basic information

Entry
Database: PDB / ID: 5ey1
TitleCrystal structure of CodY from Staphylococcus aureus with GTP and Ile
ComponentsGTP-sensing transcriptional pleiotropic repressor CodY
KeywordsTRANSCRIPTION / GTP sensing / pleiotropic transcription regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / 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 domain / GAF-like domain superfamily / Beta-Lactamase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...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 domain / GAF-like domain superfamily / Beta-Lactamase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / ISOLEUCINE / Global transcriptional regulator CodY / Global transcriptional regulator CodY
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHan, A. / Hwang, K.Y.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: The structure of the pleiotropic transcription regulator CodY provides insight into its GTP-sensing mechanism
Authors: Han, A.R. / Kang, H.R. / Son, J. / Kwon, D.H. / Kim, S. / Lee, W.C. / Song, H.K. / Song, M.J. / Hwang, K.Y.
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7816
Polymers61,4732
Non-polymers1,3094
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-23 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.824, 75.992, 166.301
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: 30736.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu3 / ATCC 700698) (bacteria)
Strain: Mu3 / ATCC 700698 / Gene: codY, SAHV_1245 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A7X1N2, UniProt: Q2FZ27*PLUS
#2: Chemical ChemComp-ILE / ISOLEUCINE / Isoleucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13NO2
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10% (v/v) 2-propanol, 0.1 M tri-sodium citrate (pH 5.0), 26% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 41162 / % possible obs: 98.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.03
Reflection shellResolution: 2→2.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.2 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHENIXmodel building
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B0L and 2B18

2b0l

2b18


Resolution: 2→29.249 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 2000 4.86 %
Rwork0.1879 --
obs0.19 41162 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 0 335 3660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083359
X-RAY DIFFRACTIONf_angle_d1.1654530
X-RAY DIFFRACTIONf_dihedral_angle_d19.6231299
X-RAY DIFFRACTIONf_chiral_restr0.046541
X-RAY DIFFRACTIONf_plane_restr0.004565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9715-2.02080.36391280.29542526X-RAY DIFFRACTION90
2.0208-2.07550.30261410.26922738X-RAY DIFFRACTION97
2.0755-2.13650.29331390.25252724X-RAY DIFFRACTION98
2.1365-2.20550.28291400.22362753X-RAY DIFFRACTION98
2.2055-2.28430.27881420.21432772X-RAY DIFFRACTION98
2.2843-2.37570.26311420.2052774X-RAY DIFFRACTION98
2.3757-2.48370.27951410.20332768X-RAY DIFFRACTION99
2.4837-2.61460.24181440.18612827X-RAY DIFFRACTION99
2.6146-2.77830.21731420.17682788X-RAY DIFFRACTION99
2.7783-2.99260.24771450.18822827X-RAY DIFFRACTION99
2.9926-3.29340.22591470.17432861X-RAY DIFFRACTION99
3.2934-3.76910.18951450.15842853X-RAY DIFFRACTION100
3.7691-4.74540.18671480.14922899X-RAY DIFFRACTION99
4.7454-29.25230.19211560.17853052X-RAY DIFFRACTION100

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