PDB-3cyn: The structure of human GPX8

ID or keywords:

Entry

Database: PDB / ID: 3cyn

Title

The structure of human GPX8

Components

Probable glutathione peroxidase 8

Keywords

OXIDOREDUCTASE / THIOREDOXIN FOLD / GLUTATHIONE PEROXIDASE / Membrane / Transmembrane / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

glutathione peroxidase / glutathione peroxidase activity / Detoxification of Reactive Oxygen Species / peroxidase activity / cellular response to oxidative stress / endoplasmic reticulum lumen / membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Kavanagh, K.L. / Johansson, C. / Yue, W.W. / Kochan, G. / Pike, A.C.W. / Murray, J. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. ...

Citation

Journal: To be Published
Title: The structure of human GPX8
Authors: Kavanagh, K.L. / Johansson, C. / Yue, W.W. / Kochan, G. / Oppermann, U.

History

Deposition	Apr 25, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 12, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _software.name
Revision 1.3	Jan 31, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4	Aug 30, 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_ref_seq_dif / 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_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	3cyn.cif.gz	124.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3cyn.ent.gz	97.2 KB	Display	PDB format
PDBx/mmJSON format	3cyn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3cyn_validation.pdf.gz	461 KB	Display	wwPDB validaton report
Full document	3cyn_full_validation.pdf.gz	461.9 KB	Display
Data in XML	3cyn_validation.xml.gz	22.8 KB	Display
Data in CIF	3cyn_validation.cif.gz	32.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cy/3cyn ftp://data.pdbj.org/pub/pdb/validation_reports/cy/3cyn	HTTPS FTP

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Related structure data

Related structure data	2p31S S: Starting model for refinement
Similar structure data	4or7-d 6pr6-d 4ele-7 4elf-8 2kym-d 4elb-6 2je2-d 4elb-2 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

2p31S

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	#104 - Aug 2008 Selenocysteine Synthase similarity (6) #212 - Aug 2017 Glutathione Transferases similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Probable glutathione peroxidase 8

B: Probable glutathione peroxidase 8

C: Probable glutathione peroxidase 8

hetero molecules

66.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Probable glutathione peroxidase 8

hetero molecules

defined by author
22.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Probable glutathione peroxidase 8

hetero molecules

defined by author
22.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Probable glutathione peroxidase 8

hetero molecules

defined by author
22.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	90.688, 120.854, 75.603
Angle α, β, γ (deg.)	90.00, 119.38, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PHE	PHE	LYS	LYS	2	A	A	47 - 90	27 - 70
2	1	PHE	PHE	LYS	LYS	2	B	B	47 - 90	27 - 70
3	1	PHE	PHE	LYS	LYS	2	C	C	47 - 90	27 - 70
4	2	GLU	GLU	SER	SER	6	A	A	91 - 99	71 - 79
5	2	GLU	GLU	SER	SER	6	B	B	91 - 99	71 - 79
6	2	GLU	GLU	SER	SER	6	C	C	91 - 99	71 - 79
7	3	HIS	HIS	VAL	VAL	2	A	A	100 - 171	80 - 151
8	3	HIS	HIS	VAL	VAL	2	B	B	100 - 171	80 - 151
9	3	HIS	HIS	VAL	VAL	2	C	C	100 - 171	80 - 151
10	4	ASN	ASN	LYS	LYS	6	A	A	172 - 179	152 - 159
11	4	ASN	ASN	LYS	LYS	6	B	B	172 - 179	152 - 159
12	4	ASN	ASN	LYS	LYS	6	C	C	172 - 179	152 - 159
13	5	PHE	PHE	PRO	PRO	2	A	A	180 - 186	160 - 166
14	5	PHE	PHE	PRO	PRO	2	B	B	180 - 186	160 - 166
15	5	PHE	PHE	PRO	PRO	2	C	C	180 - 186	160 - 166
16	6	ILE	ILE	LEU	LEU	6	A	A	187 - 209	167 - 189
17	6	ILE	ILE	LEU	LEU	6	B	B	187 - 209	167 - 189
18	6	ILE	ILE	LEU	LEU	6	C	C	187 - 209	167 - 189

#1: Protein	Probable glutathione peroxidase 8 Mass: 21885.031 Da / Num. of mol.: 3 / Fragment: residues 44-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LOC493869 / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8TED1, glutathione peroxidase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.75 Å³/Da / Density % sol: 55.26 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2 M ammonium sulfate, 1.5 % PEG 400, 0.1 M hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2008
Radiation	Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→44.99 Å / Num. all: 47649 / Num. obs: 47649 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / B_iso Wilson estimate: 29 Å² / R_merge(I) obs: 0.092 / Net I/σ(I): 8.9
Reflection shell	Resolution: 2→2.11 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.394 / Mean I/σ(I) obs: 3.1 / Num. unique all: 6901 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MAR345		data collection
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2p31

2p31

Resolution: 2→44.99 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.947 / SU B: 6.626 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.142 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1989	2404	5 %	RANDOM
R_work	0.17073	-	-	-
all	0.17217	45240	-	-
obs	0.17217	45240	99.57 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 26.557 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.22 Å²	0 Å²	0.03 Å²
2-	-	0.66 Å²	0 Å²
3-	-	-	-0.86 Å²

Refinement step

Cycle: LAST / Resolution: 2→44.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4203	0	48	242	4493

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	4373
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3082
X-RAY DIFFRACTION	r_angle_refined_deg	1.217	1.965	5920
X-RAY DIFFRACTION	r_angle_other_deg	0.892	3	7471
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.024	5	524
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.389	23.383	201
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.106	15	734
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.314	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	622
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4798
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	941
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	786
X-RAY DIFFRACTION	r_nbd_other	0.183	0.2	3059
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2094
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	2111
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	178
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	0.139	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.236	0.2	59
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.094	0.2	13
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	1.985	3	2864
X-RAY DIFFRACTION	r_mcbond_other	0.444	3	1040
X-RAY DIFFRACTION	r_mcangle_it	2.636	5	4258
X-RAY DIFFRACTION	r_scbond_it	4.361	7	1935
X-RAY DIFFRACTION	r_scangle_it	5.637	11	1660
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	721	tight positional	0.04	0.05
2	B	721	tight positional	0.04	0.05
3	C	721	tight positional	0.03	0.05
1	A	993	medium positional	0.37	0.5
2	B	993	medium positional	0.27	0.5
3	C	993	medium positional	0.29	0.5
1	A	487	loose positional	0.39	5
2	B	487	loose positional	0.56	5
3	C	487	loose positional	0.44	5
1	A	721	tight thermal	0.13	0.5
2	B	721	tight thermal	0.12	0.5
3	C	721	tight thermal	0.13	0.5
1	A	993	medium thermal	0.76	2
2	B	993	medium thermal	0.7	2
3	C	993	medium thermal	0.77	2
1	A	487	loose thermal	2.19	10
2	B	487	loose thermal	2	10
3	C	487	loose thermal	2.51	10

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	172	-
R_work	0.219	3323	-
obs	-	-	99.01 %

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	2.5528	0.5432	-1.4361	0.4063	-0.3438	2.5509	0.3163	0.3534	0.2543	-0.1392	-0.1018	-0.1129	-0.3376	-0.0574	-0.2146	0.0387	0.039	0.0661	-0.0606	0.0553	-0.0754	33.5271	109.6852	-2.3143
2	2.2448	0.267	-0.4338	1.5936	-0.0212	1.6796	0.099	0.1137	0.0996	-0.1306	0.0521	0.0407	-0.2176	-0.1973	-0.151	-0.0648	0.022	0.0271	-0.1321	0.0117	-0.1267	23.985	105.3413	10.1433
3	8.1591	7.5698	-0.9426	8.0781	-1.916	1.5103	0.0876	-0.0932	0.4504	0.0185	0.0301	0.0053	-0.1771	0.1566	-0.1176	-0.0201	-0.0685	0.0424	-0.1211	-0.0359	-0.0052	39.6476	111.1707	18.4656
4	1.4608	-1.3323	-2.4077	30.998	9.4651	9.3706	0.1778	-0.236	-0.1745	-1.4295	-0.3293	1.2451	-0.8669	1.5201	0.1515	0.1101	0.0731	-0.0192	0.1734	-0.0573	0.0665	-6.8318	125.715	31.5709
5	1.2216	0.0579	-0.2613	1.6015	0.9087	2.8095	0.0281	0.1092	-0.0047	0.0208	-0.0493	0.2323	-0.1159	-0.5371	0.0212	-0.1313	0.0938	0.0149	0.0392	0.0344	-0.0677	-0.0073	100.3137	29.2679
6	7.2667	-1.9302	-8.1711	0.785	3.0669	12.1395	0.2392	-0.0256	-0.0245	0.0409	-0.1614	0.0758	-0.2341	-0.4899	-0.0778	-0.0198	0.0746	0.0418	-0.0275	0.037	-0.0744	2.9789	104.3536	48.9396
7	18.9153	1.466	0.358	14.7184	8.0194	11.1906	-0.3764	-0.4887	0.9692	0.1828	-0.0485	0.4103	-0.8249	0.2123	0.425	0.3366	-0.1007	0.0131	0.0489	-0.0701	0.2197	-1.8674	57.043	27.5332
8	2.5134	-0.6989	-1.1427	2.6335	0.313	2.0838	-0.2378	-0.1612	-0.2471	-0.1026	0.1734	-0.0198	0.2609	-0.0588	0.0645	-0.0852	-0.033	-0.0121	-0.1117	0.0294	-0.0838	16.3099	75.1749	15.3245
9	5.5566	-5.995	-0.1458	8.5592	0.214	0.0054	-1.1449	-1.4203	-0.1423	0.9888	1.4304	-0.2435	0.2841	0.6285	-0.2855	0.1613	0.3819	-0.048	0.6567	-0.0071	-0.0489	27.8202	69.5201	27.4022

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	36 - 68	16 - 48
2	X-RAY DIFFRACTION	2	A	A	69 - 183	49 - 163
3	X-RAY DIFFRACTION	3	A	A	184 - 209	164 - 189
4	X-RAY DIFFRACTION	4	B	B	37 - 45	17 - 25
5	X-RAY DIFFRACTION	5	B	B	46 - 187	26 - 167
6	X-RAY DIFFRACTION	6	B	B	188 - 209	168 - 189
7	X-RAY DIFFRACTION	7	C	C	34 - 44	14 - 24
8	X-RAY DIFFRACTION	8	C	C	45 - 182	25 - 162
9	X-RAY DIFFRACTION	9	C	C	183 - 209	163 - 189

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