PDB-2wrt: The 2.4 Angstrom structure of the Fasciola hepatica mu class GST,...

ID or keywords:

Entry

Database: PDB / ID: 2wrt

Title

The 2.4 Angstrom structure of the Fasciola hepatica mu class GST, GST26

Components

GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

Keywords

TRANSFERASE /

PARASITE / TREMATODE

Function / homology

Function and homology information

glutathione transferase /

glutathione transferase activity /

cytoplasm
Similarity search - Function

Biological species

FASCIOLA HEPATICA (liver fluke)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Line, K. / Isupov, M.N. / LaCourse, E.J. / Brophy, P.M. / Littlechild, J.A.

Citation

Journal: To be Published
Title: The 2.5 Angstrom Structure of a Mu Class Gst from Fasciola Hepatica
Authors: Line, K. / Isupov, M.N. / Lacourse, E.J. / Brophy, P.M. / Littlechild, J.A.

History

Deposition	Sep 2, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 29, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Mar 11, 2020	Group: Derived calculations / Other Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop Item: _pdbx_database_status.status_code_sf
Revision 1.4	Dec 20, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2wrt.cif.gz	543.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2wrt.ent.gz	451.7 KB	Display	PDB format
PDBx/mmJSON format	2wrt.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wr/2wrt ftp://data.pdbj.org/pub/pdb/validation_reports/wr/2wrt	HTTPS FTP

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Related structure data

Related structure data	1fheS S: Starting model for refinement
Similar structure data	2gu6-2 1gta-d 1gtb-d 1u87-d 1m9a-d 1fhe-d 4qi2-1 2fm9-d 1ua5-d 3crt-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1fheS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (10) #255 - Mar 2021 Cisplatin and DNA similarity (10)

Deposited unit

A: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

B: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

C: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

D: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

E: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

F: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

G: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

H: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

I: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

J: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

K: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

L: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

hetero molecules

305 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

B: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

hetero molecules

defined by author&software
50.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

D: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

hetero molecules

defined by author&software
50.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

F: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

hetero molecules

defined by author&software
50.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

H: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

hetero molecules

defined by author&software
50.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

J: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

hetero molecules

defined by author&software
50.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

L: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51

defined by author&software
50.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.310, 92.501, 166.422
Angle α, β, γ (deg.)	90.00, 94.55, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	GLU	GLU	A	A	9 - 26	9 - 26
2	1	1	LYS	LYS	GLU	GLU	B	B	9 - 26	9 - 26
3	1	1	LYS	LYS	GLU	GLU	D	D	9 - 26	9 - 26
4	1	1	LYS	LYS	GLU	GLU	F	F	9 - 26	9 - 26
5	1	1	LYS	LYS	GLU	GLU	G	G	9 - 26	9 - 26
6	1	1	LYS	LYS	GLU	GLU	H	H	9 - 26	9 - 26
7	1	1	LYS	LYS	GLU	GLU	I	I	9 - 26	9 - 26
8	1	1	LYS	LYS	GLU	GLU	J	J	9 - 26	9 - 26
1	2	1	GLU	GLU	GLY	GLY	A	A	30 - 34	30 - 34
2	2	1	GLU	GLU	GLY	GLY	B	B	30 - 34	30 - 34
3	2	1	GLU	GLU	GLY	GLY	D	D	30 - 34	30 - 34
4	2	1	GLU	GLU	GLY	GLY	F	F	30 - 34	30 - 34
5	2	1	GLU	GLU	GLY	GLY	G	G	30 - 34	30 - 34
6	2	1	GLU	GLU	GLY	GLY	H	H	30 - 34	30 - 34
7	2	1	GLU	GLU	GLY	GLY	I	I	30 - 34	30 - 34
8	2	1	GLU	GLU	GLY	GLY	J	J	30 - 34	30 - 34
1	3	1	GLY	GLY	ASP	ASP	A	A	49 - 60	49 - 60
2	3	1	GLY	GLY	ASP	ASP	B	B	49 - 60	49 - 60
3	3	1	GLY	GLY	ASP	ASP	D	D	49 - 60	49 - 60
4	3	1	GLY	GLY	ASP	ASP	F	F	49 - 60	49 - 60
5	3	1	GLY	GLY	ASP	ASP	G	G	49 - 60	49 - 60
6	3	1	GLY	GLY	ASP	ASP	H	H	49 - 60	49 - 60
7	3	1	GLY	GLY	ASP	ASP	I	I	49 - 60	49 - 60
8	3	1	GLY	GLY	ASP	ASP	J	J	49 - 60	49 - 60
1	4	1	LEU	LEU	ALA	ALA	A	A	65 - 90	65 - 90
2	4	1	LEU	LEU	ALA	ALA	B	B	65 - 90	65 - 90
3	4	1	LEU	LEU	ALA	ALA	D	D	65 - 90	65 - 90
4	4	1	LEU	LEU	ALA	ALA	F	F	65 - 90	65 - 90
5	4	1	LEU	LEU	ALA	ALA	G	G	65 - 90	65 - 90
6	4	1	LEU	LEU	ALA	ALA	H	H	65 - 90	65 - 90
7	4	1	LEU	LEU	ALA	ALA	I	I	65 - 90	65 - 90
8	4	1	LEU	LEU	ALA	ALA	J	J	65 - 90	65 - 90
1	5	1	ILE	ILE	PHE	PHE	A	A	92 - 106	92 - 106
2	5	1	ILE	ILE	PHE	PHE	B	B	92 - 106	92 - 106
3	5	1	ILE	ILE	PHE	PHE	D	D	92 - 106	92 - 106
4	5	1	ILE	ILE	PHE	PHE	F	F	92 - 106	92 - 106
5	5	1	ILE	ILE	PHE	PHE	G	G	92 - 106	92 - 106
6	5	1	ILE	ILE	PHE	PHE	H	H	92 - 106	92 - 106
7	5	1	ILE	ILE	PHE	PHE	I	I	92 - 106	92 - 106
8	5	1	ILE	ILE	PHE	PHE	J	J	92 - 106	92 - 106
1	6	1	MET	MET	CYS	CYS	A	A	132 - 161	132 - 161
2	6	1	MET	MET	CYS	CYS	B	B	132 - 161	132 - 161
3	6	1	MET	MET	CYS	CYS	D	D	132 - 161	132 - 161
4	6	1	MET	MET	CYS	CYS	F	F	132 - 161	132 - 161
5	6	1	MET	MET	CYS	CYS	G	G	132 - 161	132 - 161
6	6	1	MET	MET	CYS	CYS	H	H	132 - 161	132 - 161
7	6	1	MET	MET	CYS	CYS	I	I	132 - 161	132 - 161
8	6	1	MET	MET	CYS	CYS	J	J	132 - 161	132 - 161
1	1	2	TRP	TRP	TRP	TRP	B	B	201 - 206	201 - 206
2	1	2	TRP	TRP	TRP	TRP	D	D	201 - 206	201 - 206
3	1	2	TRP	TRP	TRP	TRP	E	E	201 - 206	201 - 206
4	1	2	TRP	TRP	TRP	TRP	F	F	201 - 206	201 - 206
5	1	2	TRP	TRP	TRP	TRP	G	G	201 - 206	201 - 206
6	1	2	TRP	TRP	TRP	TRP	H	H	201 - 206	201 - 206
7	1	2	TRP	TRP	TRP	TRP	I	I	201 - 206	201 - 206
8	1	2	TRP	TRP	TRP	TRP	J	J	201 - 206	201 - 206

NCS ensembles :

ID
1
2

#1: Protein	GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME 51 / GLUTATHIONE TRANSFERASE / FH51 Mass: 25349.316 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) FASCIOLA HEPATICA (liver fluke) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P30112, glutathione transferase
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1261 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.54 % / Description: NONE
Crystal grow	Details: MDL1 CONDITION NUMBER 18 (0.2 M NA ACETATE, 0.1 M NA CACODYALTE, PH 6.5, 30% W/V PEG 8000)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
Detector	Type: ADSC CCD / Detector: CCD / Date: May 21, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.5→46.2 Å / Num. obs: 109322 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / B_iso Wilson estimate: 48.3 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 7
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 1.8 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0088	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FHE

1fhe

Resolution: 2.4→166.67 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.888 / SU B: 10.811 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.652 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28102	5463	5 %	RANDOM
R_work	0.20544	-	-	-
obs	0.20926	103778	99.82 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 40.636 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.77 Å²	0 Å²	-1.36 Å²
2-	-	0.31 Å²	0 Å²
3-	-	-	-2.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→166.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21264	0	12	1261	22537

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	21884
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.235	1.978	29507
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.33	5	2606
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.863	23.522	1025
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.873	15	3980
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.31	15	146
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	3007
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	16626
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.657	4	12996
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.951	6	20843
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.989	8	8888
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.615	10	8658
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	837	tight positional	0.03	0.05
1	2	B	837	tight positional	0.04	0.05
1	3	D	837	tight positional	0.03	0.05
1	4	F	837	tight positional	0.03	0.05
1	5	G	837	tight positional	0.04	0.05
1	6	H	837	tight positional	0.04	0.05
1	7	I	837	tight positional	0.04	0.05
1	8	J	837	tight positional	0.03	0.05
2	1	B	57	tight positional	0.02	0.05
2	2	D	57	tight positional	0.02	0.05
2	3	E	57	tight positional	0.02	0.05
2	4	F	57	tight positional	0.03	0.05
2	5	G	57	tight positional	0.03	0.05
2	6	H	57	tight positional	0.03	0.05
2	7	I	57	tight positional	0.03	0.05
2	8	J	57	tight positional	0.02	0.05
1	1	A	837	tight thermal	0.09	0.5
1	2	B	837	tight thermal	0.12	0.5
1	3	D	837	tight thermal	0.12	0.5
1	4	F	837	tight thermal	0.09	0.5
1	5	G	837	tight thermal	0.13	0.5
1	6	H	837	tight thermal	0.11	0.5
1	7	I	837	tight thermal	0.09	0.5
1	8	J	837	tight thermal	0.08	0.5
2	1	B	57	tight thermal	0.09	0.5
2	2	D	57	tight thermal	0.15	0.5
2	3	E	57	tight thermal	0.08	0.5
2	4	F	57	tight thermal	0.1	0.5
2	5	G	57	tight thermal	0.15	0.5
2	6	H	57	tight thermal	0.09	0.5
2	7	I	57	tight thermal	0.09	0.5
2	8	J	57	tight thermal	0.08	0.5

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.343	412	-
R_work	0.249	7669	-
obs	-	-	99.79 %

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