PDB-4d73: X-ray structure of a peroxiredoxin

ID or keywords:

Entry

Database: PDB / ID: 4d73

Title

X-ray structure of a peroxiredoxin

Components

(1-CYS PEROXIREDOXIN) x 2

Keywords

OXIDOREDUCTASE / ANTIOXIDANT PROTEIN / PRX5 / REDOX REGULATION

Function / homology

Function and homology information

peroxiredoxin / TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / apicoplast / thioredoxin peroxidase activity / antioxidant activity / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress ...
Similarity search - Function

Biological species

PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Staudacher, V. / Djuika, C.F. / Koduka, J. / Schlossarek, S. / Kopp, J. / Buechler, M. / Lanzer, M. / Deponte, M.

Citation

Journal: Free Radic.Biol.Med. / Year: 2015
Title: Plasmodium Falciparum Antioxidant Protein Reveals a Novel Mechanism for Balancing Turnover and Inactivation of Peroxiredoxins
Authors: Staudacher, V. / Djuika, C.F. / Koduka, J. / Schlossarek, S. / Kopp, J. / Buechler, M. / Lanzer, M. / Deponte, M.

History

Deposition	Nov 19, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 13, 2015	Provider: repository / Type: Initial release
Revision 1.1	May 20, 2015	Group: Database references
Revision 1.2	Aug 5, 2015	Group: Database references
Revision 1.3	Mar 6, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	May 8, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4d73.cif.gz	159.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4d73.ent.gz	125.8 KB	Display	PDB format
PDBx/mmJSON format	4d73.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4d73_validation.pdf.gz	430.3 KB	Display	wwPDB validaton report
Full document	4d73_full_validation.pdf.gz	431 KB	Display
Data in XML	4d73_validation.xml.gz	16.4 KB	Display
Data in CIF	4d73_validation.cif.gz	23.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d7/4d73 ftp://data.pdbj.org/pub/pdb/validation_reports/d7/4d73	HTTPS FTP

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Related structure data

Related structure data	1xiyS S: Starting model for refinement
Similar structure data	1xiy-d 6oxn-d 1oi4-d 6dwu-21 6dwu-32 6dwu-31 6dwu-15 4etj-1 6dwu-42 4qqn-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

Deposited unit

A: 1-CYS PEROXIREDOXIN

B: 1-CYS PEROXIREDOXIN

42.2 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)	41.419, 77.366, 109.751
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	1-CYS PEROXIREDOXIN Mass: 21118.924 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q5MYR6, peroxiredoxin
#2: Protein	1-CYS PEROXIREDOXIN Mass: 21070.926 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q5MYR6, peroxiredoxin
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.19 Å³/Da / Density % sol: 44 % / Description: NONE
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: PFAOPL109M WAS CRYSTALLIZED BY SITTING DROP VAPOR DIFFUSION AT 277 K WITH A RESERVOIR COMPOSITION OF 0.1 M SODIUM CITRATE PH 5.6, 13 % W/V PEG 4000, AND 18% V/V 2-PROPANOL. CRYSTALLIZATION ...Details: PFAOPL109M WAS CRYSTALLIZED BY SITTING DROP VAPOR DIFFUSION AT 277 K WITH A RESERVOIR COMPOSITION OF 0.1 M SODIUM CITRATE PH 5.6, 13 % W/V PEG 4000, AND 18% V/V 2-PROPANOL. CRYSTALLIZATION DROPS CONTAINED 250 NL 15 MG/ML PFAOPL109M MIXED WITH 500 NL RESERVOIR SOLUTION.

Crystal

Density Matthews: 2.19 Å³/Da / Density % sol: 44 % / Description: NONE

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop
Details: PFAOPL109M WAS CRYSTALLIZED BY SITTING DROP VAPOR DIFFUSION AT 277 K WITH A RESERVOIR COMPOSITION OF 0.1 M SODIUM CITRATE PH 5.6, 13 % W/V PEG 4000, AND 18% V/V 2-PROPANOL. CRYSTALLIZATION ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97239 Å / Relative weight: 1
Reflection	Resolution: 1.8→30.4 Å / Num. obs: 157758 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / B_iso Wilson estimate: 19.55 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shell	Resolution: 1.8→1.84 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XIY

1xiy

Resolution: 1.8→30.4 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 18.6 / Stereochemistry target values: ML / Details: RESIDUES A80-A86 AND B115-B119 ARE DISORDERED

	R_factor	Num. reflection	% reflection
R_free	0.1951	1662	5 %
R_work	0.1516	-	-
obs	0.1537	33206	99.21 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.1 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→30.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2823	0	0	234	3057

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2905
X-RAY DIFFRACTION	f_angle_d	1.208	3918
X-RAY DIFFRACTION	f_dihedral_angle_d	13.106	1104
X-RAY DIFFRACTION	f_chiral_restr	0.048	426
X-RAY DIFFRACTION	f_plane_restr	0.007	501

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 (%)
1.8-1.853	0.2807	149	0.218	2544	X-RAY DIFFRACTION	100
1.853-1.9128	0.2453	138	0.1982	2574	X-RAY DIFFRACTION	99
1.9128-1.9811	0.2349	158	0.1795	2581	X-RAY DIFFRACTION	99
1.9811-2.0604	0.2019	163	0.1642	2542	X-RAY DIFFRACTION	99
2.0604-2.1542	0.1948	133	0.1509	2614	X-RAY DIFFRACTION	99
2.1542-2.2677	0.2299	140	0.1465	2599	X-RAY DIFFRACTION	99
2.2677-2.4098	0.2237	119	0.1443	2635	X-RAY DIFFRACTION	100
2.4098-2.5957	0.2169	130	0.1427	2646	X-RAY DIFFRACTION	99
2.5957-2.8568	0.1879	120	0.1477	2648	X-RAY DIFFRACTION	100
2.8568-3.2697	0.1528	110	0.1429	2674	X-RAY DIFFRACTION	99
3.2697-4.1179	0.1866	137	0.1314	2702	X-RAY DIFFRACTION	100
4.1179-30.4044	0.1705	165	0.1582	2785	X-RAY DIFFRACTION	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	9.1482	-1.1229	0.8975	4.4812	-1.6522	2.2495	0.0352	0.786	-0.1022	-0.1902	0.1585	0.5124	-0.3437	-0.6075	-0.1623	0.205	0.0834	0.0427	0.2721	0.0468	0.3035	-10.0002	5.2506	-5.2477
2	2.0992	-0.1134	-1.6163	4.9745	0.268	8.3206	0.0455	-0.4141	0.2206	0.0832	0.0328	-0.1177	-0.6184	0.8159	-0.0842	0.3121	-0.0787	0.0598	0.1586	-0.0637	0.1818	6.6195	6.3333	8.1453
3	2.7193	0.3757	-0.8944	1.7572	-0.0545	1.1352	0.1349	-0.1859	0.3886	0.1592	0.0076	0.0416	-0.5079	0.1064	-0.0895	0.2786	-0.0365	0.063	0.1571	-0.0014	0.255	3.0704	6.9842	2.3438
4	0.8599	0.3504	-0.3716	3.8962	-2.2153	2.8415	-0.0554	0.0828	-0.0411	-0.3118	-0.0772	-0.2409	0.1005	0.1838	0.1552	0.1423	-0.0033	0.0225	0.1632	-0.0089	0.1609	7.9971	-6.921	-4.1206
5	1.6049	-0.109	-0.9697	2.4107	-0.7866	3.7184	0.0227	-0.0638	0.0742	0.0703	-0.0616	-0.1891	-0.1022	0.3243	0.0146	0.1457	-0.0324	0.0065	0.161	-0.0148	0.1579	6.0793	-2.8638	6.8329
6	0.8483	1.0789	0.1862	6.2792	-1.3152	1.9802	0.0202	0.0821	0.243	-0.0607	0.1698	0.4371	-0.2176	-0.3843	-0.1215	0.1298	0.0489	0.0173	0.26	0.0238	0.2384	-10.8872	-3.1775	3.4847
7	1.3141	0.8268	-0.1826	1.689	-0.5674	2.5904	0.0086	0.1178	0.0531	-0.1388	0.0768	0.1687	0.1027	-0.2405	-0.0549	0.1389	0.0032	-0.011	0.1802	0.0029	0.1617	-6.335	-9.7356	-1.4136
8	8.672	-0.2082	1.142	2.8554	-2.6532	2.6617	0.176	0.8724	0.204	-1.1177	-0.373	-0.6694	0.3267	-0.3911	0.1056	0.3925	0.0381	0.0645	0.3181	-0.0294	0.2198	2.9861	-7.9764	-16.7732
9	5.9998	-0.9474	-1.5172	1.9115	-0.0024	3.9265	-0.2467	0.0826	-0.033	-0.0351	0.0725	0.0381	0.6909	-0.2842	0.2077	0.3488	-0.1039	0.0322	0.1351	0.0029	0.1992	-5.7452	-21.7555	24.5361
10	2.6505	0.6793	-3.9605	1.8892	-1.05	5.9174	-0.0724	-0.0743	-0.0589	0.331	-0.0778	0.1552	0.1492	0.4138	0.0604	0.3305	0.0262	0.0932	0.2137	0.0054	0.2188	8.8092	-27.8162	16.9023
11	1.2085	-0.3594	-0.0892	1.0461	-0.2952	2.2101	-0.1072	-0.029	-0.2181	-0.06	0.1141	0.3278	0.8284	-0.4751	0.009	0.395	-0.1031	0.0121	0.1808	0.0134	0.2092	-5.6659	-22.3529	29.0304
12	0.7239	-0.6709	-0.2762	2.9513	-1.7311	4.6302	-0.0726	0.0315	0.0706	0.1125	-0.1199	-0.3384	-0.033	0.3105	0.1935	0.1585	-0.0285	-0.0013	0.2205	-0.0009	0.2085	6.743	-8.6171	28.198
13	5.3545	1.8638	-0.7168	5.3412	-0.9859	6.6852	-0.1348	-0.831	-0.4998	0.7742	-0.0783	-0.4253	0.4243	0.3379	0.1281	0.3302	0.071	-0.0185	0.2619	0.0516	0.2253	6.4503	-20.0924	40.4376
14	1.5685	0.1508	0.2399	2.702	-1.1433	4.5854	-0.0661	0.0311	-0.0617	-0.0619	-0.0799	-0.1042	0.3576	0.2083	0.0946	0.1464	0.0017	0.0231	0.1252	-0.0105	0.1334	3.2699	-15.5732	22.3598
15	0.8767	-0.2881	-0.1437	2.1823	-1.4845	4.1801	-0.0791	-0.1018	0.0073	0.1825	0.1485	0.1799	-0.2484	-0.5071	-0.084	0.1526	0.0056	0.0325	0.2036	-0.0147	0.1592	-7.2787	-5.0912	29.0497
16	4.1214	-0.4133	-0.5061	7.2771	-3.7496	5.1104	-0.1311	-0.5037	-0.0663	0.8685	-0.0267	-0.2931	-0.5456	0.0307	0.1243	0.2341	-0.0413	-0.0271	0.274	-0.0434	0.1543	2.6312	-6.5321	41.4319

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 59 THROUGH 68 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 69 THROUGH 78 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 79 THROUGH 108 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 109 THROUGH 139 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 140 THROUGH 172 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 173 THROUGH 183 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 184 THROUGH 227 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 228 THROUGH 238 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 63 THROUGH 77 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 78 THROUGH 89 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 90 THROUGH 108 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 109 THROUGH 127 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 128 THROUGH 139 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 140 THROUGH 172 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 173 THROUGH 220 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 221 THROUGH 237 )

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