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- PDB-4ofn: Monoclinic NaGST1 -

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Basic information

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


glutathione transferase activity / glutathione metabolic process
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 S-transferase-1
Similarity search - Component
Biological speciesNecator americanus (New World hookworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 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 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0354
Polymers47,4212
Non-polymers6152
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-17 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.554, 45.213, 113.763
Angle α, β, γ (deg.)90.00, 112.11, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 205 / Label seq-ID: 2 - 205

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Glutathione S-transferase-1


Mass: 23710.359 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
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

Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.69→105.4 Å / Num. obs: 10767 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.3
Reflection shellResolution: 2.69→2.85 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.4 / % possible all: 97.7

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Processing

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

2on7


Resolution: 2.69→14.85 Å / Cor.coef. Fo:Fc: 0.809 / Cor.coef. Fo:Fc free: 0.714 / SU B: 45.845 / SU ML: 0.459 / Cross valid method: THROUGHOUT / ESU R: 2.922 / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33036 535 4.9 %RANDOM
Rwork0.29247 ---
obs0.29436 10472 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.218 Å2
Baniso -1Baniso -2Baniso -3
1-3.75 Å20 Å20.85 Å2
2---8.21 Å2-0 Å2
3---2.84 Å2
Refinement stepCycle: LAST / Resolution: 2.69→14.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 40 24 3404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193459
X-RAY DIFFRACTIONr_bond_other_d0.0020.023333
X-RAY DIFFRACTIONr_angle_refined_deg0.9711.9814662
X-RAY DIFFRACTIONr_angle_other_deg0.89337689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0075409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.84923.827162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81315615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9751520
X-RAY DIFFRACTIONr_chiral_restr0.0550.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213845
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02807
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_it0.7981.0491642
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4471.5712049
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5571.091817
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.6078.5135134
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

Ens-ID: 1 / Number: 11972 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.69→2.761 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 47 -
Rwork0.321 669 -
obs--89.05 %
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)
12.9438-0.1638-0.17751.0615-0.07821.5693-0.01110.0631-0.1809-0.10760.05370.11880.1935-0.0705-0.04250.0329-0.0139-0.01570.51970.00110.0236-18.303-17.24113.734
20.7704-0.47660.08571.292-0.00680.6996-0.0671-0.1283-0.08740.24580.0381-0.02360.0393-0.01830.02910.0501-0.0001-0.0080.5855-0.00870.0321-9.977-21.9837.539
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 206
2X-RAY DIFFRACTION2B2 - 206

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