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- PDB-1va6: Crystal structure of Gamma-glutamylcysteine synthetase from Esche... -

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Basic information

Entry
Database: PDB / ID: 1va6
TitleCrystal structure of Gamma-glutamylcysteine synthetase from Escherichia Coli B complexed with Transition-state analogue
ComponentsGlutamate--cysteine ligase
KeywordsLIGASE / Glutathione homeostasis / Beta barrel / Peptide synthesis / Transition state analogue
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 / Chem-P2S / Glutamate--cysteine ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHibi, T. / Nii, H. / Nakatsu, T. / Kato, H. / Hiratake, J. / Oda, J.
Citation
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.
#1: 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
DepositionFeb 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,84416
Polymers116,5382
Non-polymers2,30614
Water6,233346
1
A: Glutamate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4228
Polymers58,2691
Non-polymers1,1537
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4228
Polymers58,2691
Non-polymers1,1537
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.468, 97.360, 102.185
Angle α, β, γ (deg.)90.00, 109.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 58268.844 Da / Num. of mol.: 2 / Mutation: C106S, C164S, C205S, C223S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GSH-I / Plasmid: pKGC20 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A6W9, glutamate-cysteine ligase

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Non-polymers , 5 types, 360 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-P2S / (2S)-2-AMINO-4-[[(2R)-2-CARBOXYBUTYL](PHOSPHONO)SULFONIMIDOYL]BUTANOIC ACID / N-PHOSPHORYL (2S)-2-AMINO-4-[(2S)-2-CARBOXYBUTYL-(R)-SULFONIMIDOYL]BUTANOIC ACID


Mass: 346.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19N2O8PS
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: 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: 2.78 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 2000MME, MgCl2, Tris-HCl buffer, 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: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2003
RadiationMonochromator: ROTATED-INCLINED DOUBLE-CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.8 Å / Num. all: 73644 / Num. obs: 73622 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.8
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.5 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V4G

1v4g


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.608 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.169 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3702 5 %RANDOM
Rwork0.2 ---
obs0.2 69912 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.5 Å20 Å2-2.32 Å2
2--0.64 Å20 Å2
3---0.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.319 Å
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7998 0 142 346 8486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0218339
X-RAY DIFFRACTIONr_bond_other_d00.027494
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.97511247
X-RAY DIFFRACTIONr_angle_other_deg3.658317402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.00951003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.21218
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029167
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021721
X-RAY DIFFRACTIONr_nbd_refined0.2150.51830
X-RAY DIFFRACTIONr_nbd_other0.290.58213
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1160.54178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.5613
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.150.53
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.511
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3510.550
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it3.07325026
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.42238069
X-RAY DIFFRACTIONr_scbond_it3.09623313
X-RAY DIFFRACTIONr_scangle_it4.37433178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 283
Rwork0.283 5073

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