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- PDB-4oft: C- Orthorombic NaGST1 -

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Basic information

Entry
Database: PDB / ID: 4oft
TitleC- Orthorombic 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 S-transferase-1
Similarity search - Component
Biological speciesNecator americanus (New World hookworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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 / 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase-1
B: Glutathione S-transferase-1


Theoretical massNumber of molelcules
Total (without water)47,4212
Polymers47,4212
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-13 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.630, 80.890, 200.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 1 - 206 / Label seq-ID: 1 - 206

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M sodium acetate, pH 4.6, 30% PEG 400, 100mM zinc protoporphyrin, VAPOR DIFFUSION, 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
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→100.26 Å / Num. all: 12623 / Num. obs: 12651 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.061 / Rsym value: 0.127 / Net I/σ(I): 14.9
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.15 / Rsym value: 0.461 / % possible all: 99.5

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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: 2.6→24.14 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.907 / SU B: 32.825 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26999 612 4.9 %RANDOM
Rwork0.22768 ---
obs0.22968 11972 99.79 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.345 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å2-0 Å2
2--2.53 Å20 Å2
3----3.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→24.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 0 31 3379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193430
X-RAY DIFFRACTIONr_bond_other_d0.0030.023314
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9714626
X-RAY DIFFRACTIONr_angle_other_deg0.93637644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9035410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2923.827162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92315618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6411520
X-RAY DIFFRACTIONr_chiral_restr0.0640.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213804
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02796
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_it0.9682.7681646
X-RAY DIFFRACTIONr_mcbond_other0.9672.7681645
X-RAY DIFFRACTIONr_mcangle_it1.7234.1492054
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.6962.8481784
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.32541.2775481
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: 12315 / 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: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 53 -
Rwork0.299 851 -
obs--99.23 %
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)
11.37990.0175-0.09131.8851.17544.0674-0.0431-0.0117-0.1917-0.0983-0.13520.00160.25180.03820.17830.1923-0.03990.02910.0389-0.02970.429-39.81487.783214.052
21.8340.4171-0.89991.2863-0.22695.5939-0.0097-0.3639-0.16450.0798-0.122-0.1843-00.93610.13170.1659-0.0760.01860.2221-0.00170.4633-34.8595.701237.744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 206
2X-RAY DIFFRACTION2B1 - 206

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