PDB-8bhc: K141H and S142H double mutant of hGSTA1-1

ID or keywords:

Entry

Database: PDB / ID: 8bhc

Title

K141H and S142H double mutant of hGSTA1-1

Components

Glutathione S-transferase A1

Keywords

TRANSFERASE / Thermostability / Glutathione / Detoxification / Catalysis

Function / homology

Function and homology information

Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / linoleic acid metabolic process / steroid Delta-isomerase activity / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.56 Å

Authors

Papageorgiou, A.C. / Poudel, N.

Funding support

European Union, 1items

Citation

Journal: Int J Mol Sci / Year: 2023
Title: A Key Role in Catalysis and Enzyme Thermostability of a Conserved Helix H5 Motif of Human Glutathione Transferase A1-1.
Authors: Chronopoulou, E.G. / Mutabdzija, L. / Poudel, N. / Papageorgiou, A.C. / Labrou, N.E.

History

Deposition	Oct 31, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 8, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bhc.cif.gz	438.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8bhc.ent.gz	298.9 KB	Display	PDB format
PDBx/mmJSON format	8bhc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8bhc_validation.pdf.gz	456.9 KB	Display	wwPDB validaton report
Full document	8bhc_full_validation.pdf.gz	461.5 KB	Display
Data in XML	8bhc_validation.xml.gz	41.7 KB	Display
Data in CIF	8bhc_validation.cif.gz	62.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bh/8bhc ftp://data.pdbj.org/pub/pdb/validation_reports/bh/8bhc	HTTPS FTP

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Related structure data

Related structure data	8bheC 1gseS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (11) #255 - Mar 2021 Cisplatin and DNA similarity (10) #37 - Jan 2003 Serum Albumin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1)

Deposited unit

C: Glutathione S-transferase A1

A: Glutathione S-transferase A1

D: Glutathione S-transferase A1

B: Glutathione S-transferase A1

103 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Glutathione S-transferase A1

D: Glutathione S-transferase A1

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

2

A: Glutathione S-transferase A1

B: Glutathione S-transferase A1

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

Unit cell

Length a, b, c (Å)	54.500, 93.850, 94.080
Angle α, β, γ (deg.)	90.000, 97.920, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Glutathione S-transferase A1 / 13-hydroperoxyoctadecadienoate peroxidase / Androst-5-ene-3 / 17-dione isomerase / GST HA subunit 1 ...13-hydroperoxyoctadecadienoate peroxidase / Androst-5-ene-3 / 17-dione isomerase / GST HA subunit 1 / GST class-alpha member 1 / GST-epsilon / GSTA1-1 / GTH1 Mass: 25806.275 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Cys114 was found modified in the crystal structure and modelled as CME Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P08263, glutathione transferase, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases, Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1012 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.9 % / Description: Rod-like crystals
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 20% w/v PEG 3350, 0.2 lithium citrate tribasic tetrahydrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.56→53.98 Å / Num. obs: 128429 / % possible obs: 96.6 % / Redundancy: 3.3 % / B_iso Wilson estimate: 20.76 Å² / CC_1/2: 0.99 / R_rim(I) all: 0.054 / Net I/σ(I): 13.6
Reflection shell	Resolution: 1.56→1.6 Å / Redundancy: 2.6 % / Num. unique obs: 7351 / CC_1/2: 0.51 / R_rim(I) all: 0.878 / % possible all: 74.9

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
autoXDS		data processing
Aimless		data scaling
PHASER		phasing
autoXDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1gse

1gse

Resolution: 1.56→53.98 Å / SU ML: 0.1709 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1882	6331	4.93 %
R_work	0.1648	122067	-
obs	0.166	128398	96.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 26.96 Å²

Refinement step

Cycle: LAST / Resolution: 1.56→53.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6812	0	0	1012	7824

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0065	6956
X-RAY DIFFRACTION	f_angle_d	0.9535	9360
X-RAY DIFFRACTION	f_chiral_restr	0.0511	1027
X-RAY DIFFRACTION	f_plane_restr	0.0096	1185
X-RAY DIFFRACTION	f_dihedral_angle_d	6.3613	923

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.56-1.58	0.3026	159	0.2872	2989	X-RAY DIFFRACTION	72.23
1.58-1.6	0.2997	161	0.2648	3262	X-RAY DIFFRACTION	75.85
1.6-1.62	0.2764	169	0.2469	3502	X-RAY DIFFRACTION	83.68
1.62-1.64	0.2574	209	0.2482	3715	X-RAY DIFFRACTION	89.41
1.64-1.66	0.2765	179	0.2323	4031	X-RAY DIFFRACTION	95.18
1.66-1.68	0.2493	225	0.2168	4160	X-RAY DIFFRACTION	98.61
1.68-1.7	0.2316	211	0.2096	4196	X-RAY DIFFRACTION	99.41
1.7-1.73	0.2388	210	0.2033	4139	X-RAY DIFFRACTION	99.09
1.73-1.76	0.2784	233	0.2211	4201	X-RAY DIFFRACTION	99.15
1.76-1.79	0.2462	196	0.2167	4107	X-RAY DIFFRACTION	99.12
1.79-1.82	0.2466	251	0.1992	4209	X-RAY DIFFRACTION	99.24
1.82-1.85	0.2199	225	0.1913	4142	X-RAY DIFFRACTION	99.32
1.85-1.89	0.2209	220	0.1812	4195	X-RAY DIFFRACTION	99.44
1.89-1.92	0.187	227	0.1707	4168	X-RAY DIFFRACTION	99.48
1.92-1.97	0.1938	219	0.1581	4185	X-RAY DIFFRACTION	99.59
1.97-2.01	0.1945	197	0.1578	4226	X-RAY DIFFRACTION	99.68
2.01-2.06	0.1896	192	0.1612	4198	X-RAY DIFFRACTION	99.68
2.06-2.12	0.2009	215	0.1636	4215	X-RAY DIFFRACTION	99.64
2.12-2.18	0.1962	220	0.1657	4227	X-RAY DIFFRACTION	99.35
2.18-2.25	0.1906	216	0.1566	4138	X-RAY DIFFRACTION	98.89
2.25-2.33	0.1745	213	0.1672	4161	X-RAY DIFFRACTION	98.91
2.33-2.42	0.2082	217	0.1663	4180	X-RAY DIFFRACTION	99.23
2.42-2.53	0.203	214	0.1665	4207	X-RAY DIFFRACTION	99.19
2.53-2.67	0.2097	229	0.1674	4180	X-RAY DIFFRACTION	99.37
2.67-2.83	0.1979	236	0.1673	4165	X-RAY DIFFRACTION	99.14
2.83-3.05	0.2015	236	0.1661	4159	X-RAY DIFFRACTION	98.54
3.05-3.36	0.1502	213	0.147	4170	X-RAY DIFFRACTION	98.58
3.36-3.85	0.137	193	0.1348	4235	X-RAY DIFFRACTION	98.97
3.85-4.85	0.1481	235	0.1319	4153	X-RAY DIFFRACTION	98.21
4.85-53.98	0.1806	211	0.1709	4252	X-RAY DIFFRACTION	97.74

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	4.26209945887	1.22462931374	-0.812529732534	4.44209226595	-0.193841667118	3.202159868	0.00170792791458	-0.0632877695089	0.182826835797	0.0419298899484	0.109551307474	0.401527332791	-0.330761456903	-0.248007183179	-0.0976152996081	0.204781675889	0.0271073118557	0.00555772153092	0.172600215954	-0.0121302717446	0.152266105631	-32.331919027	71.0642591015	-26.8580512364
2	0.813517613806	0.102406260706	-0.244393521714	1.08783068759	-0.139470090386	1.55295957674	0.0267716742803	-0.073158455236	-0.0526184752605	-0.00396063573138	-0.0568017318739	-0.0318911234933	-0.124365838452	0.216056003421	0.0602158247341	0.151973729922	-0.0251976531511	0.0162474796908	0.170003481427	-0.00664415598822	0.152705399906	-18.4973485092	64.670777549	-29.5900425221
3	4.49624859572	-0.424242277407	0.525163152167	3.38127914649	1.48748519831	2.88919824334	0.0503532273196	-0.350566388229	0.0477234303386	0.530138422917	0.0171011947454	0.277564255585	-0.298144887157	-0.125564335332	0.0122285089676	0.317240003796	-0.0154110536786	-0.0104544558571	0.197539600322	-0.0255168068662	0.142044301883	-23.6962568835	74.592932056	-18.7487436155
4	3.79384187814	-1.13032124759	0.963651576698	3.08857538394	0.223304742252	2.81560030719	0.0336256358008	0.133266032146	-0.247429245226	-0.0555315017081	0.0401350303862	0.200780877549	0.156791012353	-0.194416542384	-0.0259596777754	0.12893602867	-0.0197542618311	0.00434011954682	0.159934904009	-0.00928839427306	0.14310033446	-27.8549806059	16.1762527465	-21.5802432165
5	1.21832537039	-0.102806136833	0.170962781292	0.928324419371	-0.115502770565	0.80348389273	-0.00267910661665	0.00180459148381	-0.0218055514154	0.044007665944	0.00439226328863	0.0730945222256	0.0256981123981	-0.0825092526683	0.00860207988009	0.153717195255	-0.000616942860747	0.00928132945743	0.163419171038	-0.00763176181538	0.158400426224	-27.0470485989	23.1638035419	-12.6428274753
6	1.53762639866	-0.593802679689	1.98781955926	0.313521246087	-0.899781604076	2.76740880101	-0.196856095738	0.027837482399	0.285404600411	-0.0192626610875	-0.00211376222471	-0.116976810474	-0.432816651602	-0.0720142740051	0.138257196353	0.240578790614	-0.00191442213069	-0.01671625897	0.258456786081	0.0541159798101	0.281395976712	-11.1766012699	38.3591455854	-28.0820354882
7	1.88179276963	0.326722077673	-0.15741595286	1.44993779567	-0.181045185467	1.37502596681	-0.0240079409538	0.0434842812502	-0.0575040338936	0.084137398769	-0.0343755742949	-0.17315854013	-0.0059502920717	0.198109496423	0.0537989792241	0.147521772182	0.00930892545937	-0.018330572629	0.196094423372	-0.00526728226365	0.221218134645	-5.72743390032	21.8725236086	-15.2879341951
8	5.36671621077	-1.25249467689	1.60865564632	3.60237646272	0.842486898602	3.77144065968	0.170239873077	0.403633730479	0.096920503278	-0.464941497928	-0.0149027095405	-0.179080041023	-0.0108147045903	0.0706171258143	-0.0194431266218	0.189068359158	-0.0115054320029	0.037847234861	0.179326315987	-0.00635406616355	0.162700331518	-16.4621881146	13.9197557057	-26.7070956995
9	3.0533164083	-0.829813468485	1.03456129448	3.12787530383	0.226583876394	3.70380797915	0.0291310812488	0.209244724512	0.00967449990341	-0.216110049397	-0.123336189067	-0.36173789863	0.0109254041905	0.546005947076	0.109880891039	0.185522045733	0.0294943366656	0.037726954942	0.217800089687	0.0157292919004	0.191953033786	-12.8928278948	47.6879641834	-50.1025742153
10	1.1361228796	-0.192811654629	0.296512386734	1.37969222994	0.029912811918	1.53432174865	0.0187319841095	0.000470808857283	0.0244064503709	-0.114888967807	-0.00265661568098	-0.137787122257	-0.0567382553033	0.259783421498	0.0171657074435	0.1839328597	-0.0141277260577	0.0152051053816	0.205695003656	-0.00664473349881	0.170032924363	-16.81716012	56.1323469593	-43.4727945359
11	1.61283263149	-1.82753695862	1.17561700774	2.39393171853	-1.62821834565	1.05558057153	-0.21184774447	-0.302330836712	-0.0272913508301	0.304294145217	0.210036875968	0.152495957986	-0.0302487488458	-0.246971290272	-0.105715565993	0.238783585114	0.00368469996866	-0.0036614885332	0.277934103614	0.0272847790923	0.255797354922	-32.3175992584	37.5834690346	-31.7509983556
12	1.28248307869	0.176425481731	-0.250823376771	2.07322264222	-0.300844790955	1.62203802389	0.0137370540928	0.0468879740213	0.0202987800403	-0.30164014825	0.0561548307792	0.313282485959	0.0675318264792	-0.147965522695	-0.0593389708268	0.204785925219	0.00128950921152	-0.0554889898693	0.190936170252	-0.00561379336136	0.223775227784	-36.6407532884	49.6831955907	-49.2473074377
13	5.07417257119	-1.19946354352	1.12488900318	3.97654542203	0.35211024487	1.92907228748	-0.0469942983612	-0.0798714926774	-0.396081284069	-0.245659474757	-0.0147621723893	0.0268880117713	0.576616861089	-0.124838953397	-0.121965377115	0.355416743582	0.00941500776435	0.0223494944987	0.162114699507	-0.0146531281029	0.203295087951	-22.6117607888	40.5741966435	-54.2472096441
14	2.01022753794	0.416031738871	-0.682533530473	1.692033955	-0.209874858552	0.981014375816	0.0263913863636	-0.141447721895	0.104880541355	0.0960602326987	-0.0204233943466	-0.155588406686	-0.0112111509334	0.15629376694	-0.00291617344381	0.14528769983	0.00078780809687	-0.0291264705134	0.16940156763	-0.0113465561858	0.148243801468	-16.0663666309	37.9429418417	2.16477196894
15	0.337488440566	0.399012468977	-0.0843441949379	2.97542845429	-1.13201710977	1.25089093818	-0.0656787184512	0.0954792714191	0.0733941105697	-0.11299448539	0.0893911202074	0.0285389228754	-0.0185966839454	-0.0532326189859	-0.0583491057296	0.171580210793	-0.0168806111056	-0.000450148180459	0.208026782687	0.00580477887856	0.194676443768	-33.1683913657	39.9137353217	-12.3776962139
16	1.10166693911	0.187241460075	0.494922218167	1.17281659816	0.0378786794443	1.21949053909	-0.00834752227342	-0.0113446575135	0.055921177627	0.0372771301345	0.00664520804088	0.173715149751	0.0484757706664	-0.129411788082	0.0177773154226	0.141997154377	-0.0061215019228	0.0241847351107	0.193289734733	-0.00373447972143	0.191736242023	-38.2770516332	38.3257928611	0.968664677197

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'C' and (resid 1 through 37 )	C	A	1 - 37	1 - 37
2	2	chain 'C' and (resid 38 through 190 )	C	A	38 - 190	38 - 190
3	3	chain 'C' and (resid 191 through 211 )	C	A	191 - 211	191 - 211
4	4	chain 'A' and (resid 1 through 37 )	A	B	1 - 37	1 - 37
5	5	chain 'A' and (resid 38 through 107 )	A	B	38 - 107	38 - 107
6	6	chain 'A' and (resid 108 through 130 )	A	B	108 - 130	108 - 130
7	7	chain 'A' and (resid 131 through 190 )	A	B	131 - 190	131 - 190
8	8	chain 'A' and (resid 191 through 210 )	A	B	191 - 210	191 - 210
9	9	chain 'D' and (resid 1 through 37 )	D	C	1 - 37	1 - 37
10	10	chain 'D' and (resid 38 through 107 )	D	C	38 - 107	38 - 107
11	11	chain 'D' and (resid 108 through 130 )	D	C	108 - 130	108 - 130
12	12	chain 'D' and (resid 131 through 190 )	D	C	131 - 190	131 - 190
13	13	chain 'D' and (resid 191 through 210 )	D	C	191 - 210	191 - 210
14	14	chain 'B' and (resid 1 through 85 )	B	D	1 - 85	1 - 85
15	15	chain 'B' and (resid 86 through 130 )	B	D	86 - 130	86 - 130
16	16	chain 'B' and (resid 131 through 208 )	B	D	131 - 208	131 - 208

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Movie

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Structure viewers

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Viewer log

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This page

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Open data

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Basic information

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Structure visualization

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi