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- PDB-4ofm: Triclinic NaGST1 -

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Basic information

Entry
Database: PDB / ID: 4ofm
TitleTriclinic NaGST1
ComponentsGlutathione S-transferase-1
KeywordsTRANSFERASE / GST
Function / homology
Function and homology information


glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / glutathione transferase
Similarity search - Component
Biological speciesNecator americanus (New World hookworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsAsojo, O.A.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structure of glutathione S-transferase 1 from the major human hookworm parasite Necator americanus (Na-GST-1) in complex with glutathione.
Authors: Asojo, O.A. / Ceccarelli, C.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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 / struct_ncs_dom_lim / struct_site
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 / _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: Glutathione S-transferase-1
B: Glutathione S-transferase-1
C: Glutathione S-transferase-1
D: Glutathione S-transferase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0718
Polymers94,8414
Non-polymers1,2294
Water1,78399
1
A: Glutathione S-transferase-1
B: Glutathione S-transferase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0354
Polymers47,4212
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-17 kcal/mol
Surface area18600 Å2
MethodPISA
2
C: Glutathione S-transferase-1
D: Glutathione S-transferase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0354
Polymers47,4212
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-17 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.197, 47.839, 103.116
Angle α, β, γ (deg.)80.54, 78.70, 61.99
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

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
11VALVALLEULEUAA2 - 2052 - 205
21VALVALLEULEUBB2 - 2052 - 205
12VALVALLEULEUAA2 - 2052 - 205
22VALVALLEULEUCC2 - 2052 - 205
13VALVALLEULEUAA2 - 2052 - 205
23VALVALLEULEUDD2 - 2052 - 205
14METMETPHEPHEBB1 - 2061 - 206
24METMETPHEPHECC1 - 2061 - 206
15METMETPHEPHEBB1 - 2061 - 206
25METMETPHEPHEDD1 - 2061 - 206
16METMETPHEPHECC1 - 2061 - 206
26METMETPHEPHEDD1 - 2061 - 206

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Glutathione S-transferase-1


Mass: 23710.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Necator americanus (New World hookworm)
Gene: gst-1 / Production host: Komagataella pastoris (fungus) / References: UniProt: D3U1A5
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, pH 4.6, 30% PEG 400, 100mM protoporphyrin IX disodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.776
11H, H-K, H-L20.224
ReflectionResolution: 2.64→100.76 Å / Num. obs: 19062 / % possible obs: 84.8 % / Observed criterion σ(F): 2 / Redundancy: 1.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.7
Reflection shellResolution: 2.64→2.85 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 3.7 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
CrysalisProProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ON7

2on7


Resolution: 2.64→14.75 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.819 / SU B: 14.184 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26916 997 5 %RANDOM
Rwork0.21922 ---
obs0.22177 19062 91.77 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0.05 Å20.14 Å2
2--0.02 Å2-0.06 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.64→14.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6688 0 80 99 6867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196945
X-RAY DIFFRACTIONr_bond_other_d0.0070.026689
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9849358
X-RAY DIFFRACTIONr_angle_other_deg1.456315432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93623.827324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.111151233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8741540
X-RAY DIFFRACTIONr_chiral_restr0.0880.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217721
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021621
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6941.773288
X-RAY DIFFRACTIONr_mcbond_other0.6941.773287
X-RAY DIFFRACTIONr_mcangle_it1.2192.6534103
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4811.8313657
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.70312.22510732
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A119520.14
12B119520.14
21A119320.14
22C119320.14
31A117530.15
32D117530.15
41B122220.12
42C122220.12
51B120290.14
52D120290.14
61C120940.14
62D120940.14
LS refinement shellResolution: 2.64→2.711 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 20 -
Rwork0.285 402 -
obs--26.74 %

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