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- PDB-3lvw: Glutathione-inhibited ScGCL -

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Basic information

Entry
Database: PDB / ID: 3lvw
TitleGlutathione-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
GLUTATHIONE / TRIETHYLENE GLYCOL / Glutamate--cysteine ligase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBiterova, E.I. / Barycki, J.J.
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 / 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 / _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)80,6835
Polymers79,9251
Non-polymers7584
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.127, 118.127, 165.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#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
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.62 Å3/Da / Density % sol: 66.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 100mM Hepes, pH 6.8, 14-20% PEG 400, 5mM GSH, 5mM MgCl2 , VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 12, 2008 / Details: Osmic Blue
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 40046 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.77 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
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: 2.5→19.88 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.112 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25054 2000 5.1 %RANDOM
Rwork0.1991 ---
obs0.20171 37458 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.214 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2--1.04 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5476 0 50 176 5702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0225667
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9567665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51124.181287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13915962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4111534
X-RAY DIFFRACTIONr_chiral_restr0.1270.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024369
X-RAY DIFFRACTIONr_nbd_refined0.2330.22719
X-RAY DIFFRACTIONr_nbtor_refined0.3220.23896
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2334
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.26
X-RAY DIFFRACTIONr_mcbond_it1.0251.53456
X-RAY DIFFRACTIONr_mcangle_it1.7125454
X-RAY DIFFRACTIONr_scbond_it2.50232540
X-RAY DIFFRACTIONr_scangle_it3.7314.52211
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 141 -
Rwork0.29 2644 -
obs--100 %

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