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- PDB-2gwd: Crystal structure of plant glutamate cysteine ligase in complex w... -

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Basic information

Entry
Database: PDB / ID: 2gwd
TitleCrystal structure of plant glutamate cysteine ligase in complex with Mg2+ and L-glutamate
ComponentsGlutamate cysteine ligase
KeywordsLIGASE / disulfide bridges / glutathione biosynthesis / beta-hairpin / redox regulation
Function / homology
Function and homology information


oxoacid metabolic process / glutamate-cysteine ligase / glutamate-cysteine ligase activity / glutathione biosynthetic process / chloroplast / ATP binding
Similarity search - Function
Glutamate--cysteine ligase, plant-type / Glutamate--cysteine ligase, bacteria and plant / Glutamate--cysteine ligase, GCS2 / Glutamate-cysteine ligase family 2(GCS2) / Creatine Kinase; Chain A, domain 2 - #20 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GLUTAMIC ACID / Glutamate--cysteine ligase, chloroplastic
Similarity search - Component
Biological speciesBrassica juncea (brown mustard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsHothorn, M. / Wachter, A. / Gromes, R. / Stuwe, T. / Rausch, T. / Scheffzek, K.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural basis for the redox control of plant glutamate cysteine ligase.
Authors: Hothorn, M. / Wachter, A. / Gromes, R. / Stuwe, T. / Rausch, T. / Scheffzek, K.
History
DepositionMay 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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_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.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_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)51,4418
Polymers50,9741
Non-polymers4677
Water4,414245
1
A: Glutamate cysteine ligase
hetero molecules

A: Glutamate cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,88216
Polymers101,9482
Non-polymers93314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)54.810, 54.810, 518.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

DetailsThe oxidized state of the enzyme is associated with a dimeric configuration. The second part of the biological assembly is generated by X,X-Y,-Z+1/6

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Components

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


Mass: 50974.184 Da / Num. of mol.: 1 / Fragment: glutamate cysteine ligase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica juncea (brown mustard) / Gene: GSH1 / Plasmid: pETM20 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami (DE3) / References: UniProt: O23736, glutamate-cysteine ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 3350, 0.2 M magnesium acetate tetrahydrate, 0.1 M tricine, 0.05 M L-glutamate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9782 Å
DetectorType: Large Area Detector / Detector: CCD / Date: Dec 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 2.09→47.46 Å / Num. all: 27931 / Num. obs: 27931 / % possible obs: 94.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11 % / Rsym value: 0.062 / Net I/σ(I): 27.2
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 3283 / Rsym value: 0.13 / % possible all: 70.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GWC monomer

2gwc


Resolution: 2.09→47.46 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.259 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.216 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1391 5 %RANDOM
Rwork0.17532 ---
all0.178 27818 --
obs0.178 26427 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: 20.333 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.09→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 31 245 3771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223624
X-RAY DIFFRACTIONr_bond_other_d0.0010.023276
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9734902
X-RAY DIFFRACTIONr_angle_other_deg0.8123.0017604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3195441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3223.837172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9515628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1231526
X-RAY DIFFRACTIONr_chiral_restr0.0730.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
X-RAY DIFFRACTIONr_nbd_refined0.210.2761
X-RAY DIFFRACTIONr_nbd_other0.1850.23398
X-RAY DIFFRACTIONr_nbtor_refined0.180.21745
X-RAY DIFFRACTIONr_nbtor_other0.0830.21958
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.29
X-RAY DIFFRACTIONr_mcbond_it0.7221.52843
X-RAY DIFFRACTIONr_mcbond_other0.1361.5891
X-RAY DIFFRACTIONr_mcangle_it0.82123523
X-RAY DIFFRACTIONr_scbond_it1.60431698
X-RAY DIFFRACTIONr_scangle_it2.3234.51376
LS refinement shellResolution: 2.09→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 57 -
Rwork0.179 1101 -
obs-1101 100 %
Refinement TLS params.Method: refined / Origin x: 32.5849 Å / Origin y: 27.7137 Å / Origin z: 21.2128 Å
111213212223313233
T-0.0621 Å20.0596 Å20.0284 Å2--0.1116 Å20.0153 Å2---0.105 Å2
L0.8687 °2-0.3108 °20.2362 °2-0.9137 °2-0.1487 °2--0.8679 °2
S0.0298 Å °0.0825 Å °0.0442 Å °-0.1112 Å °-0.0536 Å °-0.0514 Å °0.0231 Å °0.0324 Å °0.0238 Å °

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