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- PDB-9c9r: Crystal structure of Chaetomium thermophilum Gcn2 HisRS-like doma... -

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Basic information

Entry
Database: PDB / ID: 9c9r
TitleCrystal structure of Chaetomium thermophilum Gcn2 HisRS-like domain, F1090C/G1326S variant
Componentsnon-specific serine/threonine protein kinase
KeywordsTRANSFERASE / GCN2 Integrative stress response
Function / homology
Function and homology information


eukaryotic translation initiation factor 2alpha kinase activity / DNA damage checkpoint signaling / non-specific serine/threonine protein kinase / ATP binding
Similarity search - Function
eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain / RWD domain profile. / RWD / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / : ...eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain / RWD domain profile. / RWD / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / : / Anticodon-binding domain superfamily / Ubiquitin-conjugating enzyme/RWD-like / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsBou-Nader, C. / Bahmanjah, S. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Gcn2 structurally mimics and functionally repurposes the HisRS enzyme for the integrated stress response
Authors: Bou-Nader, C. / Gaikwad, S. / Bahmanjah, S. / Zhang, F. / Hinnebusch, A.G. / Zhang, J.
History
DepositionJun 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: non-specific serine/threonine protein kinase
B: non-specific serine/threonine protein kinase


Theoretical massNumber of molelcules
Total (without water)108,4382
Polymers108,4382
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-44 kcal/mol
Surface area39050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.111, 52.714, 136.891
Angle α, β, γ (deg.)90.000, 104.272, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein non-specific serine/threonine protein kinase


Mass: 54218.883 Da / Num. of mol.: 2 / Mutation: F1090C, G1326S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0028700 / Production host: Escherichia (bacteria) / Strain (production host): Arctic
References: UniProt: G0S7T0, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 15% v/v ethylene glycol and 10% v/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.316→45.71 Å / Num. obs: 95403 / % possible obs: 99.35 % / Redundancy: 8.5 % / Biso Wilson estimate: 49.33 Å2 / CC1/2: 0.992 / Net I/σ(I): 6.41
Reflection shellResolution: 2.316→2.32 Å / Mean I/σ(I) obs: 0.96 / Num. unique obs: 49637 / CC1/2: 0.805

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→45.71 Å / SU ML: 0.3671 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.5639
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 3805 3.99 %
Rwork0.1986 91598 -
obs0.2006 95403 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.4 Å2
Refinement stepCycle: LAST / Resolution: 2.32→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7045 0 0 153 7198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727228
X-RAY DIFFRACTIONf_angle_d0.86779816
X-RAY DIFFRACTIONf_chiral_restr0.04891104
X-RAY DIFFRACTIONf_plane_restr0.00821267
X-RAY DIFFRACTIONf_dihedral_angle_d15.72692613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.350.33141340.35193371X-RAY DIFFRACTION98.23
2.35-2.380.37661620.33843378X-RAY DIFFRACTION98.31
2.38-2.410.32361500.32153313X-RAY DIFFRACTION97.77
2.41-2.450.35041330.30123365X-RAY DIFFRACTION98.56
2.45-2.480.33331280.30643398X-RAY DIFFRACTION98.11
2.48-2.520.31481450.29763327X-RAY DIFFRACTION97.61
2.52-2.560.37081280.30623363X-RAY DIFFRACTION98.62
2.56-2.610.31161330.28773335X-RAY DIFFRACTION98.3
2.61-2.660.3711600.28143427X-RAY DIFFRACTION98.03
2.66-2.710.36911270.27983314X-RAY DIFFRACTION98.23
2.71-2.760.35681490.28053391X-RAY DIFFRACTION98.69
2.76-2.820.35231310.26853389X-RAY DIFFRACTION98.93
2.82-2.890.34311550.24873387X-RAY DIFFRACTION99.47
2.89-2.960.29491380.24043422X-RAY DIFFRACTION99.19
2.96-3.040.25751580.23653391X-RAY DIFFRACTION99.52
3.04-3.130.3211240.25223424X-RAY DIFFRACTION99.63
3.13-3.230.27721630.22333358X-RAY DIFFRACTION99.66
3.23-3.350.22651240.20443469X-RAY DIFFRACTION99.78
3.35-3.480.24921710.19613404X-RAY DIFFRACTION99.78
3.48-3.640.25341230.193397X-RAY DIFFRACTION99.94
3.64-3.830.2441480.18633436X-RAY DIFFRACTION99.89
3.83-4.070.24141310.16963453X-RAY DIFFRACTION99.5
4.07-4.380.19051420.1433400X-RAY DIFFRACTION99.92
4.38-4.820.17821270.14173456X-RAY DIFFRACTION100
4.82-5.520.17771390.16113394X-RAY DIFFRACTION100
5.52-6.950.24211400.18273434X-RAY DIFFRACTION99.86
6.95-45.710.18841420.14033402X-RAY DIFFRACTION99.19

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