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

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Basic information

Entry
Database: PDB / ID: 2gwc
TitleCrystal structure of plant glutamate cysteine ligase in complex with a transition state analogue
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
Chem-BSC / Glutamate--cysteine ligase, chloroplastic
Similarity search - Component
Biological speciesBrassica juncea (brown mustard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.18 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 2.0Oct 3, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / 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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

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
E: Glutamate cysteine ligase
F: Glutamate cysteine ligase
G: Glutamate cysteine ligase
H: Glutamate cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)416,51924
Polymers414,5468
Non-polymers1,97316
Water18,3211017
1
A: Glutamate cysteine ligase
B: Glutamate cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1306
Polymers103,6372
Non-polymers4934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glutamate cysteine ligase
D: Glutamate cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1306
Polymers103,6372
Non-polymers4934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Glutamate cysteine ligase
F: Glutamate cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1306
Polymers103,6372
Non-polymers4934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Glutamate cysteine ligase
H: Glutamate cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1306
Polymers103,6372
Non-polymers4934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.040, 198.920, 114.970
Angle α, β, γ (deg.)90.00, 99.66, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 2 / Auth seq-ID: 80 - 514 / Label seq-ID: 15 - 449

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
DetailsThe oxidized state of the enzyme is associated with a dimeric configuration. The asymmetric unit contains four dimers (A-B, C-D, E-F, G-H)

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Components

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


Mass: 51818.281 Da / Num. of mol.: 8 / 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.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-BSC / (2S)-2-amino-4-(S-butylsulfonimidoyl)butanoic acid / L-BUTHIONINE-[S,R]-SULFOXIMINE


Mass: 222.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18N2O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1017 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG 3350, 0.2 M magnesium acetate tetrahydrate, 0.1 M tricine, 0.01 M L-buthionine(S,R)sulfoximine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9797, 0.9778, 0,.9737
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 2005
RadiationMonochromator: transparent diamond monochromators / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97781
301
40.97371
ReflectionResolution: 2.18→99.5 Å / Num. obs: 197271 / % possible obs: 95.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.104 / Net I/σ(I): 13.6
Reflection shellResolution: 2.18→2.27 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 40871 / Rsym value: 0.457 / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.18→99.5 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.676 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.283 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24126 9951 5 %RANDOM
Rwork0.19787 ---
all0.2 197621 --
obs0.2 187310 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: 22.442 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.01 Å2
2--0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.18→99.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28002 0 120 1017 29139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02228892
X-RAY DIFFRACTIONr_bond_other_d0.0020.0226219
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.97139093
X-RAY DIFFRACTIONr_angle_other_deg0.9163.00160896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89253511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27323.7591362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.721155037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.21915209
X-RAY DIFFRACTIONr_chiral_restr0.0830.24144
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0231973
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026032
X-RAY DIFFRACTIONr_nbd_refined0.2030.25756
X-RAY DIFFRACTIONr_nbd_other0.1880.226506
X-RAY DIFFRACTIONr_nbtor_refined0.1780.213808
X-RAY DIFFRACTIONr_nbtor_other0.0870.216204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.21153
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0620.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0730.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.2197
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.219
X-RAY DIFFRACTIONr_mcbond_it1.091.521523
X-RAY DIFFRACTIONr_mcbond_other0.2781.57133
X-RAY DIFFRACTIONr_mcangle_it0.88228081
X-RAY DIFFRACTIONr_scbond_it2.262313176
X-RAY DIFFRACTIONr_scangle_it3.0644.511001
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2545tight positional0.050.05
2B2545tight positional0.050.05
3C2545tight positional0.050.05
4D2545tight positional0.060.05
5E2545tight positional0.060.05
6F2545tight positional0.050.05
7G2545tight positional0.050.05
8H2545tight positional0.050.05
1A4146medium positional0.220.5
2B4146medium positional0.20.5
3C4146medium positional0.190.5
4D4146medium positional0.210.5
5E4146medium positional0.20.5
6F4146medium positional0.210.5
7G4146medium positional0.20.5
8H4146medium positional0.190.5
1A2545tight thermal0.110.5
2B2545tight thermal0.10.5
3C2545tight thermal0.10.5
4D2545tight thermal0.110.5
5E2545tight thermal0.110.5
6F2545tight thermal0.10.5
7G2545tight thermal0.110.5
8H2545tight thermal0.10.5
1A4146medium thermal0.482
2B4146medium thermal0.462
3C4146medium thermal0.442
4D4146medium thermal0.492
5E4146medium thermal0.52
6F4146medium thermal0.452
7G4146medium thermal0.462
8H4146medium thermal0.462
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 713 -
Rwork0.268 13142 -
obs-13142 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1408-0.0594-0.00340.47710.10130.2874-0.00660.01540.0228-0.05760.0053-0.0618-0.0755-0.02610.0013-0.0228-0.00830.0043-0.0920.0062-0.080330.554616.438935.921
20.99680.0192-0.03530.9709-0.15650.3671-0.0105-0.0269-0.0973-0.00720.0070.06890.0255-0.0570.0035-0.0537-0.0130.0033-0.03230.0143-0.0487-9.2114-2.994651.0521
30.88630.1118-0.09470.8419-0.03050.4272-0.0243-0.00050.0415-0.06960.0333-0.0586-0.03540.0807-0.009-0.0647-0.01090.0065-0.02320.034-0.039841.6304-32.516254.6724
41.0531-0.09960.19060.6502-0.18130.2371-0.03150.0825-0.0684-0.03870.03050.09050.0561-0.02820.001-0.0283-0.00960.0068-0.03650.0103-0.03461.8901-54.725444.6333
51.01960.09790.0110.9235-0.04780.4624-0.01650.07-0.0887-0.06350.010.04730.0177-0.01730.0065-0.0613-0.0061-0.0095-0.0609-0.0021-0.08820.6618-1.9769-6.0314
61.24140.02430.04730.6877-0.02180.24420.00730.11390.0852-0.0899-0.0012-0.0574-0.058-0.0347-0.006-0.02-0.00820.006-0.0390.0001-0.095640.404617.9222-20.7116
70.96240.26810.17980.79310.30360.31960.0260.0344-0.11930.07370.0103-0.19050.08960.0542-0.0363-0.02740.0083-0.0383-0.09090.0110.002-11.982445.7213.4761
81.1868-0.2177-0.14220.7734-0.00770.39270.03060.0495-0.03150.0295-0.03930.0615-0.0517-0.10430.0087-0.05740.0127-0.0135-0.0398-0.0036-0.0501-51.575367.92273.0432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA80 - 51415 - 449
2X-RAY DIFFRACTION2BB80 - 51415 - 449
3X-RAY DIFFRACTION3CC80 - 51415 - 449
4X-RAY DIFFRACTION4DD80 - 51415 - 449
5X-RAY DIFFRACTION5EE80 - 51415 - 449
6X-RAY DIFFRACTION6FF80 - 51415 - 449
7X-RAY DIFFRACTION7GG80 - 51415 - 449
8X-RAY DIFFRACTION8HH80 - 51415 - 449

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