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- PDB-7evt: Crystal structure of the N-terminal degron-truncated human glutam... -

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Basic information

Entry
Database: PDB / ID: 7evt
TitleCrystal structure of the N-terminal degron-truncated human glutamine synthetase
ComponentsGlutamine synthetase
KeywordsLIGASE / Decamer / N-terminal truncated / N-degron
Function / homology
Function and homology information


protein S-acyltransferase / Astrocytic Glutamate-Glutamine Uptake And Metabolism / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamate catabolic process / glutamine synthetase / glutamine biosynthetic process ...protein S-acyltransferase / Astrocytic Glutamate-Glutamine Uptake And Metabolism / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamate catabolic process / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / Glutamate and glutamine metabolism / glial cell projection / response to glucose / cellular response to starvation / ribosome biogenesis / cell body / angiogenesis / cell population proliferation / endoplasmic reticulum / mitochondrion / extracellular exosome / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain ...Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Glutamine synthetase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsChek, M.F. / Kim, S.Y. / Mori, T. / Hakoshima, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of N-terminal degron-truncated human glutamine synthetase.
Authors: Chek, M.F. / Kim, S.Y. / Mori, T. / Kojima, H. / Hakoshima, T.
History
DepositionMay 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase
G: Glutamine synthetase
H: Glutamine synthetase
I: Glutamine synthetase
J: Glutamine synthetase


Theoretical massNumber of molelcules
Total (without water)418,56010
Polymers418,56010
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26380 Å2
ΔGint-68 kcal/mol
Surface area126420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.917, 158.866, 118.908
Angle α, β, γ (deg.)90.000, 92.796, 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
Glutamine synthetase / / GS / Glutamate--ammonia ligase / Palmitoyltransferase GLUL


Mass: 41856.023 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLUL, GLNS / Production host: Escherichia coli (E. coli)
References: UniProt: P15104, glutamine synthetase, protein S-acyltransferase

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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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.07 M sodium citrate (pH 5.1), 10% glycerol and 5.6% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 91909 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 83.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.24
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 3.09 / Num. unique obs: 14650 / CC1/2: 0.882 / % possible all: 98.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIXv1.19.4092refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QC8

2qc8


Resolution: 2.95→44.43 Å / SU ML: 0.3624 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2496 4592 5 %
Rwork0.219 87261 -
obs0.2206 91853 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.65 Å2
Refinement stepCycle: LAST / Resolution: 2.95→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25797 0 0 0 25797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003126497
X-RAY DIFFRACTIONf_angle_d0.566236033
X-RAY DIFFRACTIONf_chiral_restr0.04093725
X-RAY DIFFRACTIONf_plane_restr0.00484842
X-RAY DIFFRACTIONf_dihedral_angle_d4.34943689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-2.980.41291440.36482730X-RAY DIFFRACTION94.73
2.98-3.020.33151520.31452893X-RAY DIFFRACTION99.97
3.02-3.050.33791550.28962934X-RAY DIFFRACTION100
3.05-3.090.30561510.2892875X-RAY DIFFRACTION99.97
3.09-3.130.31531540.28342931X-RAY DIFFRACTION99.97
3.13-3.180.34351530.28852893X-RAY DIFFRACTION99.97
3.18-3.220.35121520.2712883X-RAY DIFFRACTION99.97
3.22-3.270.32031520.27562899X-RAY DIFFRACTION100
3.27-3.320.30691530.27852914X-RAY DIFFRACTION100
3.32-3.370.28061550.27732927X-RAY DIFFRACTION99.97
3.37-3.430.29691520.27692896X-RAY DIFFRACTION99.97
3.43-3.50.2861550.25572938X-RAY DIFFRACTION100
3.5-3.560.23941520.24542895X-RAY DIFFRACTION100
3.56-3.640.29811520.24912905X-RAY DIFFRACTION99.97
3.64-3.710.29921540.25032932X-RAY DIFFRACTION100
3.71-3.80.28111540.24282917X-RAY DIFFRACTION100
3.8-3.90.24661530.23352902X-RAY DIFFRACTION100
3.9-40.24891520.22762896X-RAY DIFFRACTION100
4-4.120.26191540.21472920X-RAY DIFFRACTION100
4.12-4.250.23611530.21032914X-RAY DIFFRACTION100
4.25-4.40.25081570.19572972X-RAY DIFFRACTION100
4.4-4.580.2271500.18812859X-RAY DIFFRACTION100
4.58-4.790.2061540.18592917X-RAY DIFFRACTION100
4.79-5.040.21071530.19312913X-RAY DIFFRACTION100
5.04-5.350.23671550.19072945X-RAY DIFFRACTION100
5.36-5.770.23691530.20842903X-RAY DIFFRACTION100
5.77-6.350.27111560.21962960X-RAY DIFFRACTION100
6.35-7.260.24261530.20452925X-RAY DIFFRACTION100
7.26-9.140.21271560.18462964X-RAY DIFFRACTION99.97
9.14-44.430.18791530.18282909X-RAY DIFFRACTION97.3

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