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- PDB-2d33: Crystal Structure of gamma-Glutamylcysteine Synthetase Complexed ... -

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Basic information

Entry
Database: PDB / ID: 2d33
TitleCrystal Structure of gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride
ComponentsGlutamate--cysteine ligase
KeywordsLIGASE / glutathione homeostasis / peptide synthesis / phosphoryl transfer
Function / homology
Function and homology information


glutamate-cysteine ligase / glutamate-cysteine ligase activity / cellular response to mercury ion / glutathione biosynthetic process / cellular response to arsenic-containing substance / hyperosmotic response / ATP binding / metal ion binding / cytosol
Similarity search - Function
Helix Hairpins - #800 / Glutamate--cysteine ligase, monofunctional / Glutamate--cysteine ligase / Glutamate-cysteine ligase / Creatine Kinase; Chain A, domain 2 - #20 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / Helix Hairpins / Helix non-globular / Special ...Helix Hairpins - #800 / Glutamate--cysteine ligase, monofunctional / Glutamate--cysteine ligase / Glutamate-cysteine ligase / Creatine Kinase; Chain A, domain 2 - #20 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / Helix Hairpins / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / CYSTEINE / GLUTAMIC ACID / Glutamate--cysteine ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHibi, T. / Nakayama, M. / Nii, H. / Kurokawa, Y. / Katano, H. / Oda, J.
Citation
Journal: To be Published
Title: Structural basis of efficient coupling between peptide ligation and ATP hydrolysis by gamma-gluatamylcysteine synthetase
Authors: Hibi, T. / Nakayama, M. / Nii, H. / Kurokawa, Y. / Katano, H. / Oda, J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of gamma-glutamylcysteine synthetase: insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis.
Authors: Hibi, T. / Nii, H. / Nakatsu, T. / Kimura, A. / Kato, H. / Hiratake, J. / Oda, J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Escherichia coli B gamma-glutamylcysteine synthetase: modification, purification, crystallization and preliminary crystallographic analysis.
Authors: Hibi, T. / Hisada, H. / Nakatsu, T. / Kato, H. / Oda, J.
History
DepositionSep 25, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate--cysteine ligase
B: Glutamate--cysteine ligase
C: Glutamate--cysteine ligase
D: Glutamate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,50933
Polymers233,0754
Non-polymers3,43429
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-174 kcal/mol
Surface area73660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)325.226, 325.226, 105.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 58268.844 Da / Num. of mol.: 4 / Mutation: C106S, C164S, C205S, C223S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gshI / Plasmid: pKGC20 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A6W9, glutamate-cysteine ligase

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Non-polymers , 6 types, 375 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical
ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.78 Å3/Da / Density % sol: 74.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium formate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→49.7 Å / Num. obs: 127490 / % possible obs: 99.98 % / Redundancy: 8.2 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 8 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.4 / Num. unique all: 18611 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V4G

1v4g


Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 12.601 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19116 6408 5 %RANDOM
Rwork0.16211 ---
obs0.16356 121059 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.111 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.305 Å
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15776 0 205 346 16327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02216310
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.97422117
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66852000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89223.431749
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.143152666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.47715131
X-RAY DIFFRACTIONr_chiral_restr0.0930.22415
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212446
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.37309
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3310.511403
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.51329
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.55
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.356
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.393210245
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.136316090
X-RAY DIFFRACTIONr_scbond_it1.65926889
X-RAY DIFFRACTIONr_scangle_it2.26136027
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 477 -
Rwork0.238 8930 -
obs-8930 100 %

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