PDB-5ovq: Crystal Structure of the peroxiredoxin (AhpC2) from the Hyperther...

ID or keywords:

Entry

Database: PDB / ID: 5ovq

Title

Crystal Structure of the peroxiredoxin (AhpC2) from the Hyperthermophilic bacteria Aquifex aeolicus VF

Components

(Peroxiredoxin) x 2

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

thioredoxin-dependent peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / cell redox homeostasis / cytosol
Similarity search - Function

Biological species

Aquifex aeolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Warkentin, E. / Peng, G.

Citation

Journal: Biochim Biophys Acta Gen Subj / Year: 2018
Title: Structural properties of the peroxiredoxin AhpC2 from the hyperthermophilic eubacterium Aquifex aeolicus.
Authors: Liu, W. / Liu, A. / Gao, H. / Wang, Q. / Wang, L. / Warkentin, E. / Rao, Z. / Michel, H. / Peng, G.

History

Deposition	Aug 29, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 10, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / 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 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ovq.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb5ovq.ent.gz	878 KB	Display	PDB format
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Validation report

Summary document	5ovq_validation.pdf.gz	513.7 KB	Display	wwPDB validaton report
Full document	5ovq_full_validation.pdf.gz	534.5 KB	Display
Data in XML	5ovq_validation.xml.gz	107.1 KB	Display
Data in CIF	5ovq_validation.cif.gz	148.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ov/5ovq ftp://data.pdbj.org/pub/pdb/validation_reports/ov/5ovq	HTTPS FTP

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Related structure data

Related structure data	3w6gS S: Starting model for refinement
Similar structure data	7cqj-d 5ucx-2 5ucx-1 3233 6iu0-1 5xbr-1 6itz-1 4mh3-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	#137 - May 2011 Cytochrome bc1 similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: Peroxiredoxin

B: Peroxiredoxin

C: Peroxiredoxin

D: Peroxiredoxin

E: Peroxiredoxin

F: Peroxiredoxin

G: Peroxiredoxin

H: Peroxiredoxin

I: Peroxiredoxin

J: Peroxiredoxin

K: Peroxiredoxin

L: Peroxiredoxin

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, verified by electron microscopy.

Unit cell

Length a, b, c (Å)	51.100, 141.500, 143.000
Angle α, β, γ (deg.)	61.00, 79.40, 80.90
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))
2	1	(chain B and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))
3	1	(chain C and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))
4	1	(chain D and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))
5	1	(chain E and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))
6	1	(chain F and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))
7	1	(chain G and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))
8	1	(chain H and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))
9	1	(chain I and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))
10	1	(chain J and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))
11	1	(chain K and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))
12	1	(chain L and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))

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	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	GLY	GLY	(chain A and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	A	A	6 - 10	6 - 10
1	2	PRO	PRO	PHE	PHE	(chain A and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	A	A	12 - 79	12 - 79
1	3	HIS	HIS	VAL	VAL	(chain A and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	A	A	81 - 222	81 - 222
2	1	LEU	LEU	GLY	GLY	(chain B and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	B	B	6 - 10	6 - 10
2	2	PRO	PRO	PHE	PHE	(chain B and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	B	B	12 - 79	12 - 79
2	3	HIS	HIS	VAL	VAL	(chain B and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	B	B	81 - 222	81 - 222
3	1	LEU	LEU	GLY	GLY	(chain C and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	C	C	6 - 10	6 - 10
3	2	PRO	PRO	PHE	PHE	(chain C and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	C	C	12 - 79	12 - 79
3	3	HIS	HIS	VAL	VAL	(chain C and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	C	C	81 - 222	81 - 222
4	1	LEU	LEU	GLY	GLY	(chain D and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	D	D	6 - 10	6 - 10
4	2	PRO	PRO	PHE	PHE	(chain D and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	D	D	12 - 79	12 - 79
4	3	HIS	HIS	VAL	VAL	(chain D and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	D	D	81 - 222	81 - 222
5	1	LEU	LEU	GLY	GLY	(chain E and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	E	E	6 - 10	6 - 10
5	2	PRO	PRO	PHE	PHE	(chain E and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	E	E	12 - 79	12 - 79
5	3	HIS	HIS	VAL	VAL	(chain E and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	E	E	81 - 222	81 - 222
6	1	LEU	LEU	GLY	GLY	(chain F and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	F	F	6 - 10	6 - 10
6	2	PRO	PRO	PHE	PHE	(chain F and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	F	F	12 - 79	12 - 79
6	3	HIS	HIS	VAL	VAL	(chain F and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	F	F	81 - 222	81 - 222
7	1	LEU	LEU	GLY	GLY	(chain G and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	G	G	6 - 10	6 - 10
7	2	PRO	PRO	PHE	PHE	(chain G and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	G	G	12 - 79	12 - 79
7	3	HIS	HIS	VAL	VAL	(chain G and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	G	G	81 - 222	81 - 222
8	1	LEU	LEU	GLY	GLY	(chain H and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	H	H	6 - 10	6 - 10
8	2	PRO	PRO	PHE	PHE	(chain H and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	H	H	12 - 79	12 - 79
8	3	HIS	HIS	VAL	VAL	(chain H and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	H	H	81 - 222	81 - 222
9	1	LEU	LEU	GLY	GLY	(chain I and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	I	I	6 - 10	6 - 10
9	2	PRO	PRO	PHE	PHE	(chain I and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	I	I	12 - 79	12 - 79
9	3	HIS	HIS	VAL	VAL	(chain I and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	I	I	81 - 222	81 - 222
10	1	LEU	LEU	GLY	GLY	(chain J and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	J	J	6 - 10	6 - 10
10	2	PRO	PRO	PHE	PHE	(chain J and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	J	J	12 - 79	12 - 79
10	3	HIS	HIS	VAL	VAL	(chain J and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	J	J	81 - 222	81 - 222
11	1	LEU	LEU	GLY	GLY	(chain K and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	K	K	6 - 10	6 - 10
11	2	PRO	PRO	PHE	PHE	(chain K and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	K	K	12 - 79	12 - 79
11	3	HIS	HIS	VAL	VAL	(chain K and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	K	K	81 - 222	81 - 222
12	1	LEU	LEU	GLY	GLY	(chain L and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	L	L	6 - 10	6 - 10
12	2	PRO	PRO	PHE	PHE	(chain L and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	L	L	12 - 79	12 - 79
12	3	HIS	HIS	VAL	VAL	(chain L and (resid 6 through 10 or resid 12 through 79 or resid 81 through 222))	L	L	81 - 222	81 - 222

#1: Protein	Peroxiredoxin Mass: 25455.107 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / References: UniProt: O67024, peroxiredoxin
#2: Protein	Peroxiredoxin Mass: 25384.029 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / References: UniProt: O67024, peroxiredoxin
#3: Chemical	ChemComp-UNL / UNKNOWN LIGAND Mass: 72.106 Da / Num. of mol.: 11 / Source method: isolated from a natural source
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1559 / 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: 2.92 Å³/Da / Density % sol: 57.81 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCI, pH 8.5, 1.4 M Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 24, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→20 Å / Num. obs: 306783 / % possible obs: 96.3 % / Redundancy: 3.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.072 / Net I/σ(I): 12.2
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.68 / Mean I/σ(I) obs: 2.48 / Num. unique obs: 45076 / CC_1/2: 0.845 / % possible all: 94.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3W6G

3w6g

Resolution: 1.8→19.987 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 31.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2143	15324	5 %
R_work	0.1855	-	-
obs	0.1869	306553	96.39 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→19.987 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21154	0	55	1559	22768

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	21845
X-RAY DIFFRACTION	f_angle_d	0.901	29792
X-RAY DIFFRACTION	f_dihedral_angle_d	12.19	13009
X-RAY DIFFRACTION	f_chiral_restr	0.06	3254
X-RAY DIFFRACTION	f_plane_restr	0.008	3815

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	12752	X-RAY DIFFRACTION	6.417	TORSIONAL
1	2	B	12752	X-RAY DIFFRACTION	6.417	TORSIONAL
1	3	C	12752	X-RAY DIFFRACTION	6.417	TORSIONAL
1	4	D	12752	X-RAY DIFFRACTION	6.417	TORSIONAL
1	5	E	12752	X-RAY DIFFRACTION	6.417	TORSIONAL
1	6	F	12752	X-RAY DIFFRACTION	6.417	TORSIONAL
1	7	G	12752	X-RAY DIFFRACTION	6.417	TORSIONAL
1	8	H	12752	X-RAY DIFFRACTION	6.417	TORSIONAL
1	9	I	12752	X-RAY DIFFRACTION	6.417	TORSIONAL
1	10	J	12752	X-RAY DIFFRACTION	6.417	TORSIONAL
1	11	K	12752	X-RAY DIFFRACTION	6.417	TORSIONAL
1	12	L	12752	X-RAY DIFFRACTION	6.417	TORSIONAL

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 (%)
1.8-1.8204	0.3564	503	0.33	9559	X-RAY DIFFRACTION	94
1.8204-1.8418	0.3143	493	0.303	9362	X-RAY DIFFRACTION	94
1.8418-1.8643	0.3477	494	0.2904	9384	X-RAY DIFFRACTION	94
1.8643-1.8879	0.3164	509	0.2858	9705	X-RAY DIFFRACTION	95
1.8879-1.9127	0.299	498	0.2786	9531	X-RAY DIFFRACTION	95
1.9127-1.9389	0.312	503	0.2601	9561	X-RAY DIFFRACTION	95
1.9389-1.9665	0.2915	516	0.2529	9788	X-RAY DIFFRACTION	96
1.9665-1.9959	0.288	502	0.2376	9535	X-RAY DIFFRACTION	96
1.9959-2.027	0.2689	511	0.2302	9710	X-RAY DIFFRACTION	96
2.027-2.0602	0.2609	512	0.2283	9728	X-RAY DIFFRACTION	96
2.0602-2.0957	0.2416	507	0.2113	9627	X-RAY DIFFRACTION	96
2.0957-2.1338	0.2551	517	0.2186	9834	X-RAY DIFFRACTION	96
2.1338-2.1748	0.2568	506	0.2141	9600	X-RAY DIFFRACTION	97
2.1748-2.2191	0.2453	516	0.2068	9797	X-RAY DIFFRACTION	96
2.2191-2.2673	0.2356	511	0.1989	9717	X-RAY DIFFRACTION	97
2.2673-2.32	0.2318	514	0.1909	9799	X-RAY DIFFRACTION	97
2.32-2.3779	0.2273	510	0.1905	9679	X-RAY DIFFRACTION	97
2.3779-2.4421	0.2379	517	0.186	9844	X-RAY DIFFRACTION	97
2.4421-2.5138	0.2273	512	0.1858	9706	X-RAY DIFFRACTION	97
2.5138-2.5948	0.2053	517	0.179	9824	X-RAY DIFFRACTION	97
2.5948-2.6873	0.2244	519	0.1885	9869	X-RAY DIFFRACTION	97
2.6873-2.7946	0.2138	510	0.1807	9688	X-RAY DIFFRACTION	97
2.7946-2.9215	0.2235	519	0.1876	9856	X-RAY DIFFRACTION	97
2.9215-3.075	0.2026	515	0.174	9794	X-RAY DIFFRACTION	98
3.075-3.2668	0.1943	518	0.1728	9826	X-RAY DIFFRACTION	98
3.2668-3.5178	0.1898	518	0.1663	9852	X-RAY DIFFRACTION	98
3.5178-3.8695	0.1839	516	0.1634	9791	X-RAY DIFFRACTION	97
3.8695-4.4242	0.1682	507	0.1448	9631	X-RAY DIFFRACTION	96
4.4242-5.5541	0.1681	518	0.1542	9856	X-RAY DIFFRACTION	98
5.5541-19.9879	0.1939	516	0.1705	9776	X-RAY DIFFRACTION	97

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	0.1425	-0.081	-0.0629	0.7917	0.2881	0.6858	0.0095	0.0117	-0.0305	-0.1474	0.0025	-0.0444	-0.1165	-0.0052	0.0089	0.0538	-0.0268	-0.0241	0.2682	-0.0187	0.2438	99.6335	-3.556	-44.8959
2	0.2041	-0.0029	0.0002	0.691	-0.7847	1.6987	-0.0498	-0.0156	-0.0496	0.2562	0.0293	0.0239	0.0881	-0	0.027	0.5117	0.0522	0.0505	0.2059	0.005	0.2236	87.1835	-6.1677	6.594
3	0.2962	-0.2108	-0.1029	2.1374	0.5207	0.5512	-0.0014	-0.0503	0.03	-0.2959	0.0298	-0.0951	0.1488	0.0606	-0.0246	0.5334	0.025	0.065	0.2389	0.0148	0.2223	111.285	-47.8626	-71.6741
4	0.2875	0.1939	-0.4276	1.0125	-1.0866	1.8416	-0.018	0.0366	0.0202	-0.2461	-0.0435	-0.1059	0.0026	-0.0024	0.0536	0.6016	0.0367	0.0413	0.2303	0.0161	0.2385	110.4925	-94.6865	-46.9074
5	0.4505	-0.3682	-0.5063	0.8871	0.7108	1.4769	-0.0704	-0.0468	-0.0111	0.2197	0.0012	0.0929	-0.0031	-0.0029	0.0714	0.5236	0.0124	0.0364	0.2087	0.0142	0.2198	97.6272	-97.2338	4.5603
6	0.2673	-0.2551	-0.0697	1.3812	0.1687	0.2257	-0.0449	0.0254	-0.0256	0.2559	0.0586	0.1042	-0.0882	-0.0228	-0.0208	0.942	0.0674	0.0672	0.2921	0.0242	0.3011	85.9314	-52.982	31.3343

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and (resid 7 through 220 )) or (chain 'B' and (resid 7 through 220 ))
2	X-RAY DIFFRACTION	2	(chain 'C' and (resid 7 through 220 )) or (chain 'D' and (resid 7 through 220 ))
3	X-RAY DIFFRACTION	3	(chain 'E' and (resid 7 through 220 )) or (chain 'F' and (resid 7 through 220 ))
4	X-RAY DIFFRACTION	4	(chain 'G' and (resid 7 through 220 )) or (chain 'H' and (resid 7 through 220 ))
5	X-RAY DIFFRACTION	5	(chain 'I' and (resid 7 through 220 )) or (chain 'J' and (resid 7 through 220 ))
6	X-RAY DIFFRACTION	6	(chain 'K' and (resid 7 through 220 )) or (chain 'L' and (resid 7 through 220 ))

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