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- PDB-5oes: The structure of a glutathione synthetase (StGSS1) from Solanum t... -

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Basic information

Entry
Database: PDB / ID: 5oes
TitleThe structure of a glutathione synthetase (StGSS1) from Solanum tuberosum in ADP and y-EC bound closed conformation.
ComponentsGlutathione synthetase
KeywordsPLANT PROTEIN / Glutathione synthetase
Function / homology
Function and homology information


glutathione synthase / glutathione synthase activity / glutathione binding / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
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 ...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
GAMMA-GLUTAMYLCYSTEINE / ADENOSINE-5'-DIPHOSPHATE / Glutathione synthetase
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsLilley, C.J. / Maqbool, A. / Wu, D. / Yusup, H.B. / Jones, L.M. / Birch, P.R.J. / Banfield, M.J. / Urwin, P.E. / Eves-van den Akker, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M014207/1 United Kingdom
CitationJournal: PLoS Genet. / Year: 2018
Title: Effector gene birth in plant parasitic nematodes: Neofunctionalization of a housekeeping glutathione synthetase gene.
Authors: Lilley, C.J. / Maqbool, A. / Wu, D. / Yusup, H.B. / Jones, L.M. / Birch, P.R.J. / Banfield, M.J. / Urwin, P.E. / Eves-van den Akker, S.
History
DepositionJul 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_ncs_dom_lim
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.ptnr2_auth_asym_id / _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.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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione synthetase
B: Glutathione synthetase
C: Glutathione synthetase
D: Glutathione synthetase
E: Glutathione synthetase
F: Glutathione synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,68228
Polymers326,3746
Non-polymers4,30822
Water7,224401
1
A: Glutathione synthetase
B: Glutathione synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2199
Polymers108,7912
Non-polymers1,4287
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-33 kcal/mol
Surface area36460 Å2
MethodPISA
2
C: Glutathione synthetase
D: Glutathione synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,24410
Polymers108,7912
Non-polymers1,4528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-43 kcal/mol
Surface area36670 Å2
MethodPISA
3
E: Glutathione synthetase
F: Glutathione synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2199
Polymers108,7912
Non-polymers1,4287
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-39 kcal/mol
Surface area36800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.390, 154.390, 344.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPVALVALAA14 - 48314 - 483
21ASPASPVALVALBB14 - 48314 - 483
12ASPASPLEULEUAA14 - 48214 - 482
22ASPASPLEULEUCC14 - 48214 - 482
13ASPASPLEULEUAA14 - 48214 - 482
23ASPASPLEULEUDD14 - 48214 - 482
14ASPASPVALVALAA14 - 48314 - 483
24ASPASPVALVALEE14 - 48314 - 483
15ASPASPVALVALAA14 - 48314 - 483
25ASPASPVALVALFF14 - 48314 - 483
16ASPASPLEULEUBB14 - 48214 - 482
26ASPASPLEULEUCC14 - 48214 - 482
17ASPASPVALVALBB14 - 48314 - 483
27ASPASPVALVALDD14 - 48314 - 483
18ASPASPVALVALBB14 - 48314 - 483
28ASPASPVALVALEE14 - 48314 - 483
19ASPASPVALVALBB14 - 48314 - 483
29ASPASPVALVALFF14 - 48314 - 483
110VALVALLEULEUCC13 - 48213 - 482
210VALVALLEULEUDD13 - 48213 - 482
111ASPASPVALVALCC14 - 48314 - 483
211ASPASPVALVALEE14 - 48314 - 483
112ASPASPVALVALCC14 - 48314 - 483
212ASPASPVALVALFF14 - 48314 - 483
113ASPASPVALVALDD14 - 48314 - 483
213ASPASPVALVALEE14 - 48314 - 483
114ASPASPVALVALDD14 - 48314 - 483
214ASPASPVALVALFF14 - 48314 - 483
115ASPASPVALVALEE14 - 48314 - 483
215ASPASPVALVALFF14 - 48314 - 483

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Glutathione synthetase / GSH-S


Mass: 54395.699 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Plasmid: pOPINS3C / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle / References: UniProt: M1CSC4, glutathione synthase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-3GC / GAMMA-GLUTAMYLCYSTEINE


Mass: 250.272 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H14N2O5S
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 3.14 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.4 M D-malic acid with the addition of 2.5 mM y-EC, 2.5 mM ADP, 5 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 143724 / % possible obs: 99.8 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.145 / Rrim(I) all: 0.154 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 1.238 / Rrim(I) all: 1.309

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KAL

3kal


Resolution: 2.48→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.486 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.241
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 7240 4.9 %RANDOM
Rwork0.2241 ---
obs0.2249 140946 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.58 Å2 / Biso mean: 49.843 Å2 / Biso min: 22.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å2-0 Å2-0 Å2
2--2.5 Å2-0 Å2
3----4.99 Å2
Refinement stepCycle: final / Resolution: 2.48→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21465 0 268 401 22134
Biso mean--67.95 41.08 -
Num. residues----2680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01922133
X-RAY DIFFRACTIONr_bond_other_d0.0010.0220701
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.97929942
X-RAY DIFFRACTIONr_angle_other_deg0.922348051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03152660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65224.311058
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.588154009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.10715169
X-RAY DIFFRACTIONr_chiral_restr0.0750.23357
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02124197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024344
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A290760.05
12B290760.05
21A289720.05
22C289720.05
31A289000.06
32D289000.06
41A290080.06
42E290080.06
51A290740.05
52F290740.05
61B288740.05
62C288740.05
71B287980.06
72D287980.06
81B289660.05
82E289660.05
91B290860.06
92F290860.06
101C287620.06
102D287620.06
111C288720.06
112E288720.06
121C290880.05
122F290880.05
131D288620.06
132E288620.06
141D289060.06
142F289060.06
151E289000.06
152F289000.06
LS refinement shellResolution: 2.475→2.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 571 -
Rwork0.417 10245 -
all-10816 -
obs--99.8 %
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)
11.5976-0.1754-0.24760.4791-0.04811.4113-0.0351-0.3068-0.07360.03760.03490.0022-0.016-0.07090.00020.00850.01230.02280.08650.02510.165.304443.0624149.4294
21.13820.3039-0.15770.65090.21881.6031-0.05820.1869-0.1236-0.06040.1173-0.00370.01180.1319-0.05910.017-0.02510.01690.083-0.01060.095490.682842.0409108.7954
30.567-0.0646-0.00131.1830.36981.1191-0.03740.06170.0573-0.21150.03180.0582-0.0222-0.09760.00550.16440.0059-0.04460.0274-0.01960.191444.771165.139986.3414
40.64-0.17690.07361.36190.44511.66350.0844-0.00730.0240.0611-0.00720.0857-0.16040.0253-0.07710.12060.02850.01410.0231-0.0460.217843.529490.8197126.8868
50.5795-0.05830.02331.8122-0.7011.42070.00880.0160.0713-0.0240.0344-0.0646-0.2462-0.0276-0.04310.1316-0.03140.0040.02450.02680.1707112.147689.1511130.954
60.58610.24420.17811.0742-0.65791.98540.0386-0.09050.0150.2915-0.0496-0.0991-0.16530.08930.0110.1407-0.0256-0.02830.03870.00470.1489112.718563.8121171.7854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 499
2X-RAY DIFFRACTION2B14 - 499
3X-RAY DIFFRACTION3C12 - 499
4X-RAY DIFFRACTION4D13 - 499
5X-RAY DIFFRACTION5E14 - 499
6X-RAY DIFFRACTION6F14 - 499

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