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- PDB-2on5: Structure of NaGST-2 -

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Basic information

Entry
Database: PDB / ID: 2on5
TitleStructure of NaGST-2
ComponentsNa Glutathione S-transferase 2
KeywordsTRANSFERASE / GST / hookworm / Necator
Function / homology
Function and homology information


transferase activity
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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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-2
Similarity search - Component
Biological speciesNecator americanus (New World hookworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAsojo, O.A. / Ngamelue, M. / Homma, H. / Goud, G. / Zhan, B. / Hotez, P.J.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: X-ray structures of Na-GST-1 and Na-GST-2 two glutathione s-transferase from the human hookworm Necator americanus
Authors: Asojo, O.A. / Homma, K. / Sedlacek, M. / Ngamelue, M. / Goud, G.N. / Zhan, B. / Deumic, V. / Asojo, O. / Hotez, P.J.
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2011Group: Non-polymer description
Revision 1.3Mar 21, 2012Group: Non-polymer description
Revision 1.4Aug 30, 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.end_auth_comp_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: Na Glutathione S-transferase 2
B: Na Glutathione S-transferase 2
C: Na Glutathione S-transferase 2
D: Na Glutathione S-transferase 2
E: Na Glutathione S-transferase 2
F: Na Glutathione S-transferase 2
G: Na Glutathione S-transferase 2
H: Na Glutathione S-transferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,52192
Polymers189,3468
Non-polymers7,17684
Water31,9051771
1
A: Na Glutathione S-transferase 2
G: Na Glutathione S-transferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,19224
Polymers47,3362
Non-polymers1,85622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na Glutathione S-transferase 2
C: Na Glutathione S-transferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,13023
Polymers47,3362
Non-polymers1,79421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Na Glutathione S-transferase 2
F: Na Glutathione S-transferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,19224
Polymers47,3362
Non-polymers1,85622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Na Glutathione S-transferase 2
H: Na Glutathione S-transferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,00621
Polymers47,3362
Non-polymers1,67019
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.916, 107.921, 166.990
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / 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: 5 / Auth seq-ID: 1 - 206 / Label seq-ID: 1 - 206

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

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Components

#1: Protein
Na Glutathione S-transferase 2 / NaGST-2


Mass: 23668.207 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Necator americanus (New World hookworm)
Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / References: UniProt: D3U1A6*PLUS
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 76 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1771 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→33 Å / Num. all: 161446 / Num. obs: 142281 / % possible obs: 88.1 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.073 / Rsym value: 0.062 / Net I/σ(I): 13.1
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.39 / Rsym value: 0.407 / % possible all: 50.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TW9

1tw9


Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.159 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22702 7090 5 %RANDOM
Rwork0.17798 ---
obs0.1804 135157 88.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.494 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.34 Å2
2--0.36 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13400 0 464 1771 15635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02214148
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9918896
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47751640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70623.457648
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.744152432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5531580
X-RAY DIFFRACTIONr_chiral_restr0.1040.21920
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210672
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.27491
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.29531
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.21593
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8511.58541
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.182213208
X-RAY DIFFRACTIONr_scbond_it2.28336472
X-RAY DIFFRACTIONr_scangle_it3.3574.55688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A824medium positional0.240.5
2B824medium positional0.240.5
3C824medium positional0.250.5
4D824medium positional0.190.5
5E824medium positional0.180.5
6F824medium positional0.120.5
7G824medium positional0.250.5
8H824medium positional0.130.5
1A851loose positional0.645
2B851loose positional0.585
3C851loose positional0.715
4D851loose positional0.575
5E851loose positional0.715
6F851loose positional0.685
7G851loose positional0.745
8H851loose positional0.545
1A824medium thermal1.882
2B824medium thermal1.832
3C824medium thermal1.062
4D824medium thermal1.792
5E824medium thermal1.752
6F824medium thermal1.372
7G824medium thermal1.032
8H824medium thermal1.312
1A851loose thermal2.7310
2B851loose thermal2.6510
3C851loose thermal2.0810
4D851loose thermal2.6410
5E851loose thermal2.8310
6F851loose thermal2.1610
7G851loose thermal2.1610
8H851loose thermal2.110
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 396 -
Rwork0.234 8187 -
obs--72.41 %
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)
10.4938-0.1661-0.01990.6401-0.1250.5862-0.0076-0.0559-0.0126-0.02820.0009-0.051-0.0050.03380.0067-0.0656-0.0073-0.0149-0.07850.0027-0.119428.6642.00842.945
20.68180.19110.09250.8437-0.10670.7024-0.00580.08140.01760.0106-0.0048-0.04360.01250.02850.0106-0.07050.0118-0.0117-0.07570.0013-0.120128.67651.79440.545
30.84060.24990.27860.79920.05450.7278-0.01-0.00590.14450.0943-0.00140.1233-0.0238-0.04190.0114-0.06190.00760.0066-0.09870.0056-0.07668.16862.54251.374
41.238-0.055-0.46420.71470.4571.8525-0.0519-0.2241-0.14550.0793-0.02910.04590.2170.00860.0811-0.0291-0.0046-0.0148-0.04450.0276-0.109614.99728.83476.24
51.12520.06280.40590.65860.42061.7449-0.04720.21240.1306-0.0742-0.02860.0285-0.2141-0.0130.0758-0.02680.0057-0.0164-0.04660.0259-0.109915.0124.9637.238
60.7978-0.3133-0.06280.66630.07850.76530.0109-0.12860.0410.0111-0.0064-0.084-0.09160.2025-0.0045-0.0418-0.0447-0.01710.0219-0.0052-0.121235.36443.23881.408
70.7406-0.2242-0.34270.83230.02930.7655-0.01580.0115-0.1431-0.0923-0.00320.1170.0376-0.03950.019-0.0631-0.0072-0.0437-0.09270.0036-0.07788.192-8.72832.089
80.75340.35290.05430.71610.11610.693-0.00210.1252-0.0351-0.01510.0041-0.06890.08560.1954-0.002-0.04950.0428-0.01370.027-0.0001-0.119735.37310.5452.085
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2061 - 206
2X-RAY DIFFRACTION2BB1 - 2061 - 206
3X-RAY DIFFRACTION3CC1 - 2061 - 206
4X-RAY DIFFRACTION4DD1 - 2061 - 206
5X-RAY DIFFRACTION5EE1 - 2061 - 206
6X-RAY DIFFRACTION6FF1 - 2061 - 206
7X-RAY DIFFRACTION7GG1 - 2061 - 206
8X-RAY DIFFRACTION8HH1 - 2061 - 206

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