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- PDB-5oev: The structure of a glutathione synthetase like-effector (GSS22) f... -

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Basic information

Entry
Database: PDB / ID: 5oev
TitleThe structure of a glutathione synthetase like-effector (GSS22) from Globodera pallida in apoform.
ComponentsGlutathione synthetase-like effector 22 (Gpa-GSS22-apo)
KeywordsTRANSFERASE / Plant-parasitic nematode / Effector / Glutathione synthetase-like
Function / homology
Function and homology information


glutathione synthase activity / glutathione binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Glutathione synthase, N-terminal, eukaryotic / Glutathione synthase, C-terminal, eukaryotic / Glutathione synthase / Eukaryotic glutathione synthase, ATP binding domain
Similarity search - Domain/homology
Glutathione synthetase
Similarity search - Component
Biological speciesGlobodera pallida (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-like effector 22 (Gpa-GSS22-apo)
B: Glutathione synthetase-like effector 22 (Gpa-GSS22-apo)
C: Glutathione synthetase-like effector 22 (Gpa-GSS22-apo)
D: Glutathione synthetase-like effector 22 (Gpa-GSS22-apo)


Theoretical massNumber of molelcules
Total (without water)229,7214
Polymers229,7214
Non-polymers00
Water6,575365
1
A: Glutathione synthetase-like effector 22 (Gpa-GSS22-apo)
C: Glutathione synthetase-like effector 22 (Gpa-GSS22-apo)


Theoretical massNumber of molelcules
Total (without water)114,8612
Polymers114,8612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-7 kcal/mol
Surface area35580 Å2
MethodPISA
2
B: Glutathione synthetase-like effector 22 (Gpa-GSS22-apo)
D: Glutathione synthetase-like effector 22 (Gpa-GSS22-apo)


Theoretical massNumber of molelcules
Total (without water)114,8612
Polymers114,8612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-9 kcal/mol
Surface area35880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.258, 122.393, 132.769
Angle α, β, γ (deg.)90.000, 97.610, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 8 - 487 / Label seq-ID: 31 - 510

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Glutathione synthetase-like effector 22 (Gpa-GSS22-apo)


Mass: 57430.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Globodera pallida (invertebrata) / Cell: Dorsal Gland Cell / Gene: GSS22 / Plasmid: pOPINS3C / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle / References: UniProt: A0A183CD52*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.2 M tri-methylamine N-oxide, 0.1 M Tris pH 9 and 20 % w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 99955 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.076 / Net I/σ(I): 17
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.839 / Rrim(I) all: 0.903

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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: 2.18→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.52 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.198
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.237 5118 5 %RANDOM
Rwork0.2152 ---
obs0.2163 97815 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.6 Å2 / Biso mean: 46.949 Å2 / Biso min: 25.14 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å20 Å2-0.09 Å2
2--1.05 Å2-0 Å2
3---1.15 Å2
Refinement stepCycle: final / Resolution: 2.18→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13470 0 0 365 13835
Biso mean---47.51 -
Num. residues----1693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01913706
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212927
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.96218490
X-RAY DIFFRACTIONr_angle_other_deg0.908329959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74351673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88424.294652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.548152490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6911591
X-RAY DIFFRACTIONr_chiral_restr0.0750.22091
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022735
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A248620.08
12B248620.08
21A252080.07
22C252080.07
31A282400.09
32D282400.09
41B251440.08
42C251440.08
51B248300.09
52D248300.09
61C249500.08
62D249500.08
LS refinement shellResolution: 2.178→2.235 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 357 -
Rwork0.371 7221 -
all-7578 -
obs--99.91 %
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)
10.4901-0.24420.11021.3962-0.33840.71980.04240.1180.0939-0.1792-0.07520.1468-0.0984-0.08210.03280.0670.0214-0.02190.0720.00130.055815.7464146.773628.034
21.58740.257-0.39281.2228-0.34250.7456-0.0951-0.2027-0.34410.1726-0.0086-0.07210.16890.12280.10370.13090.0544-0.00610.10410.01130.108610.49685.028232.5534
31.1339-0.19190.09850.6776-0.28131.0997-0.0408-0.1146-0.19660.0797-0.01580.05370.20360.00920.05660.0705-0.00710.02950.03280.01820.041527.6079112.047757.583
40.8508-0.35040.29121.1209-0.10530.90150.0130.08680.2704-0.1862-0.017-0.1329-0.18490.05560.0040.112-0.01290.00620.02370.02420.11143.3184119.87412.0508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 487
2X-RAY DIFFRACTION2B8 - 487
3X-RAY DIFFRACTION3C8 - 487
4X-RAY DIFFRACTION4D8 - 487

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