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- PDB-3lvv: BSO-inhibited ScGCL -

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Basic information

Entry
Database: PDB / ID: 3lvv
TitleBSO-inhibited ScGCL
ComponentsGlutamate--cysteine ligase
KeywordsLIGASE / glutathione / atp-grasp / atp-binding / glutathione biosynthesis / nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


glutamate-cysteine ligase / glutamate-cysteine ligase activity / glutathione biosynthetic process / response to cadmium ion / response to hydrogen peroxide / ATP binding / cytoplasm
Similarity search - Function
Glutamate cysteine ligase subdomain / Helicase, Ruva Protein; domain 3 - #960 / Creatine Kinase; Chain A, domain 2 - #50 / Glutamate-cysteine ligase catalytic subunit / Glutamate-cysteine ligase / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / Helicase, Ruva Protein; domain 3 / DNA polymerase; domain 1 / 2-Layer Sandwich ...Glutamate cysteine ligase subdomain / Helicase, Ruva Protein; domain 3 - #960 / Creatine Kinase; Chain A, domain 2 - #50 / Glutamate-cysteine ligase catalytic subunit / Glutamate-cysteine ligase / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / Helicase, Ruva Protein; domain 3 / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-LBP / TRIETHYLENE GLYCOL / Glutamate--cysteine ligase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBarycki, J.J. / Biterova, E.I.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis for feedback and pharmacological inhibition of Saccharomyces cerevisiae glutamate cysteine ligase.
Authors: Biterova, E.I. / Barycki, J.J.
History
DepositionFeb 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8787
Polymers79,9251
Non-polymers9536
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.863, 117.863, 165.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate--cysteine ligase / Gamma-glutamylcysteine synthetase / Gamma-ECS / GCS


Mass: 79925.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GSH1, J0832, YJL101C / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2(DE3)PLYSS / References: UniProt: P32477, glutamate-cysteine ligase

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Non-polymers , 5 types, 283 molecules

#2: Chemical ChemComp-LBP / (2S)-2-amino-4-(S-butyl-N-phosphonosulfonimidoyl)butanoic acid


Mass: 302.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19N2O6PS
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 100 mM Hepes, pH 6.8, 12% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 59891 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IG5

3ig5


Resolution: 2.2→38.35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.432 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23851 1651 3.3 %RANDOM
Rwork0.18113 ---
obs0.18302 48184 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.713 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2--1.25 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5476 0 58 277 5811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225692
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.967694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8525671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.224.181287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58115962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8521534
X-RAY DIFFRACTIONr_chiral_restr0.1220.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024366
X-RAY DIFFRACTIONr_nbd_refined0.2250.22843
X-RAY DIFFRACTIONr_nbtor_refined0.3160.23932
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2435
X-RAY DIFFRACTIONr_metal_ion_refined0.0340.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.212
X-RAY DIFFRACTIONr_mcbond_it1.051.53439
X-RAY DIFFRACTIONr_mcangle_it1.77325459
X-RAY DIFFRACTIONr_scbond_it2.71332561
X-RAY DIFFRACTIONr_scangle_it3.8414.52235
LS refinement shellResolution: 2.2→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 110 -
Rwork0.261 3181 -
obs--76.78 %

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