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- PDB-3kaj: Apoenzyme structure of homoglutathione synthetase from Glycine ma... -

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Basic information

Entry
Database: PDB / ID: 3kaj
TitleApoenzyme structure of homoglutathione synthetase from Glycine max in open conformation
ComponentsHomoglutathione synthetase
KeywordsLIGASE / Dimer / ATP-grasp domain
Function / homology
Function and homology information


glutathione synthase / glutathione synthase activity / glutathione binding / magnesium ion binding / ATP binding
Similarity search - Function
Glutathione synthase lid domain / Dna Ligase; domain 1 - #80 / Glutathione Synthetase; Chain A, domain 3 / Glutathione Synthetase; Chain A, domain 3 / Glutathione synthase, substrate-binding domain superfamily, eukaryotic / Glutathione synthase, substrate-binding domain / Eukaryotic glutathione synthase / Glutathione synthase, alpha-helical / Glutathione synthase, substrate-binding domain superfamily / Glutathione synthase, N-terminal, eukaryotic ...Glutathione synthase lid domain / Dna Ligase; domain 1 - #80 / Glutathione Synthetase; Chain A, domain 3 / Glutathione Synthetase; Chain A, domain 3 / Glutathione synthase, substrate-binding domain superfamily, eukaryotic / Glutathione synthase, substrate-binding domain / Eukaryotic glutathione synthase / Glutathione synthase, alpha-helical / Glutathione synthase, substrate-binding domain superfamily / Glutathione synthase, N-terminal, eukaryotic / Glutathione synthase, C-terminal, eukaryotic / Glutathione synthase / Eukaryotic glutathione synthase, ATP binding domain / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutathione synthetase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGalant, A. / Arkus, K.A.J. / Zubieta, C. / Cahoon, R.E. / Jez, J.M.
CitationJournal: Plant Cell / Year: 2009
Title: Structural Basis for Evolution of Product Diversity in Soybean Glutathione Biosynthesis.
Authors: Galant, A. / Arkus, K.A. / Zubieta, C. / Cahoon, R.E. / Jez, J.M.
History
DepositionOct 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homoglutathione synthetase
B: Homoglutathione synthetase


Theoretical massNumber of molelcules
Total (without water)111,4532
Polymers111,4532
Non-polymers00
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-14 kcal/mol
Surface area38050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.957, 80.549, 89.995
Angle α, β, γ (deg.)90.00, 96.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Homoglutathione synthetase


Mass: 55726.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: hGS / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9M426, glutathione synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3000, 0.1 M 3-(N-morpholino)-2-hydroxypropanesulfonic acid (MOPSO), pH 7, 0.2 M MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2007
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→28.4 Å / Num. all: 62342 / Num. obs: 59099 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.069 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 8652 / Rsym value: 0.379 / % possible all: 86.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human glutathione synthetase, 2HGS

2hgs


Resolution: 2→28.38 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.894 / SU B: 4.992 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.218 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26859 3031 5 %RANDOM
Rwork0.19795 ---
all0.20151 59099 --
obs0.20151 57570 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.989 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→28.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7108 0 0 469 7577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0227443
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0321.96910087
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1125928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27624.132334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.714151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7081551
X-RAY DIFFRACTIONr_chiral_restr0.1790.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025576
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2580.23959
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25194
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2571
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2571.54746
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96427428
X-RAY DIFFRACTIONr_scbond_it2.9333105
X-RAY DIFFRACTIONr_scangle_it4.344.52659
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 201 -
Rwork0.218 3815 -
obs-3815 100 %

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