PDB-3vwv: crystal structure of N-terminally truncated peroxiredoxin 4 from ...

ID or keywords:

Entry

Database: PDB / ID: 3vwv

Title

crystal structure of N-terminally truncated peroxiredoxin 4 from M. musculus

Components

Peroxiredoxin-4

Keywords

OXIDOREDUCTASE /

peroxiredoxin family / thioredoxin fold /

peroxiredoxin

Function / homology

Function and homology information

negative regulation of male germ cell proliferation / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / molecular sequestering activity / protein maturation by protein folding /

smooth endoplasmic reticulum / reactive oxygen species metabolic process / Neutrophil degranulation / extracellular matrix organization / cell redox homeostasis ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Inaba, K. / Suzuki, M.

Citation

Journal: Sci Rep / Year: 2013
Title: Synergistic cooperation of PDI family members in peroxiredoxin 4-driven oxidative protein folding
Authors: Sato, Y. / Kojima, R. / Okumura, M. / Hagiwara, M. / Masui, S. / Maegawa, K. / Saiki, M. / Horibe, T. / Suzuki, M. / Inaba, K.

History

Deposition	Sep 3, 2012	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 4, 2013	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3vwv.cif.gz	170.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3vwv.ent.gz	144.3 KB	Display	PDB format
PDBx/mmJSON format	3vwv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vw/3vwv ftp://data.pdbj.org/pub/pdb/validation_reports/vw/3vwv	HTTPS FTP

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Related structure data

Related structure data	3vwuC 3vwwC 3w8jC 2pn8 C: citing same article (ref.)
Similar structure data	7m15-3 4tmx-2 7an4-2 2b9u-1 4tmz-2 4ncn-2 4tn1-1 4tmt-1 4tmt-2 3dsb-d Search similar-shape structures by Omokage search (details) 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	#80 - Aug 2006 AAA+ Proteases similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #88 - Apr 2007 Clathrin similarity (1) #4 - Apr 2000 Collagen similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #166 - Oct 2013 Proteasome similarity (1) #176 - Aug 2014 Dynein similarity (1) #177 - Sep 2014 Apoptosomes similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#80 - Aug 2006
AAA+ Proteases
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (1)
#88 - Apr 2007
Clathrin
similarity (1)
#4 - Apr 2000
Collagen
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#166 - Oct 2013
Proteasome
similarity (1)
#176 - Aug 2014
Dynein
similarity (1)
#177 - Sep 2014
Apoptosomes
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)
#116 - Aug 2009
Sulfotransferases
similarity (1)

Deposited unit

A: Peroxiredoxin-4

B: Peroxiredoxin-4

hetero molecules

47.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	104.321, 104.321, 84.228
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

#1: Protein	Peroxiredoxin-4 / / Antioxidant enzyme AOE372 / Peroxiredoxin IV / Prx-IV / Thioredoxin peroxidase AO372 / Thioredoxin- ...Antioxidant enzyme AOE372 / Peroxiredoxin IV / Prx-IV / Thioredoxin peroxidase AO372 / Thioredoxin-dependent peroxide reductase A0372 Mass: 23613.787 Da / Num. of mol.: 2 / Fragment: UNP residues 87-274 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prdx4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08807, peroxiredoxin
#2: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#3: Chemical	ChemComp-ACY / ACETIC ACID / Acetic acid Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.43 Å³/Da / Density % sol: 49.3 %
Crystal grow	Temperature: 293 K / Method: evaporation / pH: 4.6 Details: 30% PEG 400, 100mM NaOAc (pH 4.6), 100mM CaCl2, EVAPORATION, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 6, 2011
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 1.8→40.81 Å / Num. obs: 41798 / % possible obs: 99.9 % / Redundancy: 7.6 % / B_iso Wilson estimate: 17.05 Å²
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 7.4 % / % possible all: 99.5

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Processing

Software

Name	Version	Classification
BSS		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→40.81 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9019 / SU ML: 0.17 / σ(F): 1.97 / Phase error: 17.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1932	2133	5.1 %
R_work	0.1532	-	-
obs	0.1552	41783	99.85 %

Solvent computation

Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 45.589 Å² / k_sol: 0.38 e/Å³

Displacement parameters

B_iso max: 86.65 Å² / B_iso mean: 23.8799 Å² / B_iso min: 5.78 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.0332 Å²	-0 Å²	0 Å²
2-	-	-3.0332 Å²	-0 Å²
3-	-	-	6.0664 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→40.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2911	0	18	367	3296

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	3168
X-RAY DIFFRACTION	f_angle_d	1.469	4313
X-RAY DIFFRACTION	f_dihedral_angle_d	15.835	1190
X-RAY DIFFRACTION	f_chiral_restr	0.12	460
X-RAY DIFFRACTION	f_plane_restr	0.008	564

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7997-1.8415	0.2317	142	0.1931	2594	2736	99
1.8415-1.8876	0.2217	136	0.1754	2674	2810	100
1.8876-1.9386	0.2127	140	0.1635	2619	2759	100
1.9386-1.9957	0.19	155	0.1564	2609	2764	100
1.9957-2.0601	0.1851	163	0.1569	2616	2779	100
2.0601-2.1337	0.1935	123	0.1548	2660	2783	100
2.1337-2.2191	0.1732	137	0.1468	2646	2783	100
2.2191-2.3201	0.1937	139	0.1391	2646	2785	100
2.3201-2.4424	0.1847	140	0.1461	2625	2765	100
2.4424-2.5954	0.193	124	0.1576	2650	2774	100
2.5954-2.7958	0.2394	159	0.1676	2654	2813	100
2.7958-3.077	0.2044	160	0.1714	2613	2773	100
3.077-3.5221	0.1926	127	0.1495	2692	2819	100
3.5221-4.4366	0.169	137	0.1349	2671	2808	100
4.4366-40.8219	0.1853	151	0.1505	2681	2832	99

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	6.5929	-4.3319	-3.294	3.5767	3.5209	4.6795	0.0638	-0.0063	-0.4913	-0.0282	-0.3331	1.5122	0.6969	-0.8447	0.3648	0.4049	-0.1057	0.0192	0.3423	-0.0067	0.7302	20.9848	-2.7332	27.0392
2	1.0691	0.2629	0.1825	5.0088	-0.5115	1.5055	-0.0148	0.2013	-0.012	-0.8839	0.0381	0.1468	0.1215	0.0299	-0.0345	0.2023	-0.0027	0.0039	0.1486	-0.0031	0.0815	29.7092	10.0816	16.7937
3	1.9444	-1.2563	-1.5521	3.9023	1.4178	1.5165	-0.0314	0.0024	-0.0166	-0.1141	0.0226	-0.1459	0.0054	0.0313	0.0449	0.0779	0.0134	-0.001	0.0764	0.0334	0.058	35.488	13.0569	27.4562
4	3.7552	-1.9333	-2.5763	8.0722	5.3336	4.2828	0.0777	0.2226	0.3033	-0.4471	0.2109	-0.6713	-0.0233	0.0775	-0.2875	0.099	0.0033	0.0153	0.1215	0.0068	0.1795	46.3747	11.6415	22.7139
5	1.9823	-1.0705	-0.2633	2.5725	0.5628	0.5123	-0.0156	0.1024	0.1096	-0.3007	-0.0102	-0.1714	0.0389	0.0216	0.0278	0.1134	0.0123	0.0156	0.0949	0.0201	0.0511	33.6139	18.9801	23.8451
6	4.6053	0.4824	0.5533	2.7875	-1.2487	7.7179	-0.1593	-0.1169	0.129	-0.2592	0.2653	-0.582	-0.2668	0.6799	-0.0536	0.059	-0.0385	0.0184	0.0718	-0.0069	0.2334	42.4432	25.4764	27.7361
7	2.4505	-0.5583	-0.8044	3.4759	1.5277	1.87	-0.1267	-0.0201	0.0059	0.0185	0.062	0.1241	0.2179	-0.0155	0.0664	0.1076	0.0018	-0.0132	0.0799	0.0279	0.0529	28.0547	9.0076	27.3443
8	4.9749	4.1939	2.8696	7.3673	5.1087	7.1821	0.167	-0.2194	0.1185	0.6776	-0.1093	-0.1714	0.4258	-0.1828	-0.0231	0.1545	0.0165	-0.0218	0.0817	0.0224	0.0932	37.0609	2.8959	31.4584
9	3.2976	0.1088	-0.622	4.4299	5.5244	8.2375	-0.0706	0.0842	-0.0017	0.519	0.6357	-0.787	0.7486	1.1147	-0.4151	0.2165	0.0874	-0.015	0.1874	0.0082	0.1961	46.036	-1.5295	23.2179
10	4.6248	-3.5436	2.754	8.077	-1.9464	7.2428	0.0939	0.972	-0.0478	-1.0722	-0.4341	-1.7677	-0.3765	0.595	0.3292	0.3263	0.0441	0.1079	0.4015	0.0271	0.4232	43.3368	-24.0659	22.5936
11	4.7382	4.9425	4.4581	5.1768	4.7153	4.4718	0.3777	0.0843	0.5982	-0.2949	-0.6582	0.633	-0.7058	-0.2832	0.4024	0.3694	0.0635	0.0136	0.2903	-0.0437	0.4128	22.5089	1.3235	36.0036
12	1.8118	-1.0058	-0.3411	6.9098	-1.2516	2.1161	0.0771	-0.1123	0.0929	0.6314	-0.0151	-0.062	-0.1527	-0.0013	-0.0762	0.0772	-0.011	-0.0306	0.1037	-0.0046	0.0773	28.048	-12.56	42.841
13	1.0177	0.6624	0.3568	3.9914	1.7784	0.8361	0.092	-0.1905	-0.1102	0.6925	-0.0826	0.4173	0.1611	0.0436	-0.0044	0.2008	-0.0278	-0.0083	0.1577	0.0316	0.0812	29.3127	-18.1362	47.3277
14	2.0739	2.3116	2.4092	5.5042	3.5729	3.2141	0.0303	0.0335	-0.0465	-0.0414	0.0588	-0.2129	0.026	0.063	-0.0487	0.0693	-0.0036	0.0109	0.09	0.0402	0.0628	34.0442	-16.6652	33.7028
15	3.2335	2.2743	3.3704	4.1015	4.9996	6.4074	0.0647	0.0503	-0.41	0.0541	0.2016	-0.5054	0.0346	0.2548	-0.2404	0.0913	0.001	0.0285	0.1515	0.0197	0.2562	45.0674	-16.3778	38.5377
16	1.7082	2.0221	0.4147	4.3974	1.12	0.3159	0.1157	-0.1309	-0.1222	0.3066	-0.072	-0.1223	0.129	-0.0408	-0.0565	0.1033	-0.0144	-0.0156	0.0994	0.0228	0.0584	31.9337	-21.8376	37.8036
17	5.2385	-0.2776	0.1494	3.5365	-0.9513	7.7883	0.0326	0.1907	-0.2311	0.1818	0.2044	-0.7222	0.6496	0.5604	-0.1128	0.1084	0.0398	-0.0054	0.0792	0.007	0.2345	39.572	-29.7974	33.5294
18	4.152	-0.1863	0.3669	4.1634	-0.0931	4.19	-0.0108	0.1521	0.0909	-0.1532	-0.0097	0.2136	-0.1585	-0.2429	0.0252	0.0852	-0.0034	0.0008	0.0582	0.0082	0.0756	24.0529	-14.6488	31.3235
19	5.6637	-1.4027	-1.4208	5.5394	0.5579	7.7706	-0.1297	-0.364	0.2242	0.0033	0.2592	-0.1099	-0.3165	0.3838	-0.078	0.1145	-0.0168	-0.0275	0.0586	0.0345	0.078	34.8086	-4.7244	40.0599
20	4.5545	-0.5719	-0.2171	8.3779	5.537	4.8772	-0.0172	0.2897	-0.3604	-0.7478	0.1515	-0.4691	-0.2212	0.1566	-0.1305	0.2047	-0.0179	0.0488	0.1087	0.0283	0.1775	36.5956	-6.746	29.6978
21	4.8537	-0.4667	-1.3766	7.4668	4.807	7.54	-0.3809	0.0994	-0.223	-0.4156	0.3322	-0.4204	-0.2144	0.4957	0.0705	0.1475	-0.0473	0.0301	0.1306	0.0505	0.2457	46.2444	-3.2624	37.8851
22	2.4287	1.5215	-2.8237	0.9941	-1.6978	3.8129	0.0923	-0.4509	0.509	0.2525	-0.2283	-0.6409	0.1763	-0.177	0.0919	0.1449	-0.0472	-0.067	0.2664	-0.0724	0.3376	44.3798	21.7905	39.0485

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 74:83)	A	74 - 83
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 84:109)	A	84 - 109
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 110:128)	A	110 - 128
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 129:144)	A	129 - 144
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 145:163)	A	145 - 163
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 164:177)	A	164 - 177
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 178:213)	A	178 - 213
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 214:224)	A	214 - 224
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 225:244)	A	225 - 244
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 245:255)	A	245 - 255
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 75:84)	B	75 - 84
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 85:99)	B	85 - 99
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 100:109)	B	100 - 109
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 110:128)	B	110 - 128
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 129:144)	B	129 - 144
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 145:163)	B	145 - 163
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 164:177)	B	164 - 177
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 178:203)	B	178 - 203
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 204:213)	B	204 - 213
20	X-RAY DIFFRACTION	20	chain 'B' and (resseq 214:224)	B	214 - 224
21	X-RAY DIFFRACTION	21	chain 'B' and (resseq 225:244)	B	225 - 244
22	X-RAY DIFFRACTION	22	chain 'B' and (resseq 245:257)	B	245 - 257

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