PDB-1h4o: Monoclinic form of human peroxiredoxin 5

ID or keywords:

Entry

Database: PDB / ID: 1h4o

Title

Monoclinic form of human peroxiredoxin 5

Components

PEROXIREDOXIN 5

Keywords

OXIDOREDUCTASE / ANTIOXIDANT ENZYME / THIOREDOXIN PEROTHIOREDOXIN / FOLDXIDASE

Function / homology

Function and homology information

peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Detoxification of Reactive Oxygen Species ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIR / Resolution: 1.95 Å

Authors

Declercq, J.P. / Evrard, C.

Citation

Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of Human Peroxiredoxin 5, a Novel Type of Mammalian Peroxiredoxin at 1.5 A Resolution
Authors: Declercq, J.P. / Evrard, C. / Clippe, A. / Stricht, D.V. / Bernard, A. / Knoops, B.

History

Deposition	May 11, 2001	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 23, 2001	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 5, 2014	Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1h4o.cif.gz	261.5 KB	Display	PDBx/mmCIF format
PDB format	pdb1h4o.ent.gz	223.4 KB	Display	PDB format
PDBx/mmJSON format	1h4o.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/h4/1h4o ftp://data.pdbj.org/pub/pdb/validation_reports/h4/1h4o	HTTPS FTP

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Related structure data

Related structure data	1hd2C C: citing same article (ref.)
Similar structure data	4k7o-1 3drn-2 4k7o-3 7bgx-d 1oc3-2 2mu1-d 1w8m-d 4mmm-2 1hd2-d 4mmm-1 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) 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) 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

1hd2C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#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: PEROXIREDOXIN 5

B: PEROXIREDOXIN 5

C: PEROXIREDOXIN 5

D: PEROXIREDOXIN 5

E: PEROXIREDOXIN 5

F: PEROXIREDOXIN 5

G: PEROXIREDOXIN 5

H: PEROXIREDOXIN 5

hetero molecules

136 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PEROXIREDOXIN 5

hetero molecules

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

2

B: PEROXIREDOXIN 5

hetero molecules

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

3

C: PEROXIREDOXIN 5

hetero molecules

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

4

D: PEROXIREDOXIN 5

hetero molecules

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

5

E: PEROXIREDOXIN 5

hetero molecules

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

6

F: PEROXIREDOXIN 5

hetero molecules

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

7

G: PEROXIREDOXIN 5

hetero molecules

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

8

H: PEROXIREDOXIN 5

hetero molecules

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

Unit cell

Length a, b, c (Å)	130.790, 66.490, 141.240
Angle α, β, γ (deg.)	90.00, 117.54, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.270446, -0.953291, 0.134518), (0.950263, -0.286741, -0.12157), (0.154464, 0.094949, 0.983425)	-31.456, 4.38, -28.61
2	given	(-0.985374, 0.163467, 0.048136), (-0.161289, -0.985829, 0.046121), (0.054993, 0.037683, 0.997775)	-29.8, 27.764, -63.289
3	given	(0.100545, 0.992969, -0.06248), (-0.993238, 0.103839, 0.05192), (0.058042, 0.056838, 0.996695)	-6.783, 26.291, -95.794
4	given	(0.986253, -0.142584, -0.083513), (0.138721, 0.989048, -0.050397), (0.089784, 0.03812, 0.995232)	-62.012, 13.213, 4.178
5	given	(-0.097589, -0.994769, 0.030188), (0.993386, -0.099208, -0.057815), (0.060508, 0.024346, 0.997871)	-21.284, 64.635, -32.178
6	given	(-0.999018, -0.01047, 0.043054), (0.010323, -0.99994, -0.003643), (0.043089, -0.003195, 0.999066)	30.05, 27.226, -63.802
7	given	(0.25684, 0.961914, -0.093568), (-0.954999, 0.267466, 0.128215), (0.148358, 0.056427, 0.987323)	-23.777, -38.257, -90.625

#1: Protein	PEROXIREDOXIN 5 / / PRDX5 / PRXV / AOEB166 / PMP20 / ARC1 Mass: 16919.514 Da / Num. of mol.: 8 / Fragment: RESIDUES 54-214 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LUNG / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: P30044, peroxiredoxin
#2: Chemical	ChemComp-BEZ / BENZOIC ACID / Benzoic acid Mass: 122.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₇H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1213 / 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: 3.75 Å³/Da / Density % sol: 67 % / Description: NCS AVERAGING
Crystal grow	pH: 5.3 Details: PROTEIN WAS CRYSTALLIZED FROM 1.6 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE BUFFER PH 5.3, 0.2 M POTASSIUM SODIUM TARTRATE, 1 MM DTT, 0.02 % (W/V) SODIUM AZIDE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978766
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2000 / Details: TWO MIRRORS
Radiation	Monochromator: FLAT AND N2 COOLED AND SAGITTALY BENT MONOCHROMATORS Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978766 Å / Relative weight: 1
Reflection	Resolution: 1.95→24 Å / Num. obs: 151926 / % possible obs: 96.6 % / Redundancy: 1.83 % / R_merge(I) obs: 0.032 / Net I/σ(I): 21
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.142 / Mean I/σ(I) obs: 5 / % possible all: 96.6

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM		phasing
REFMAC	5	refinement

Refinement

Method to determine structure:

SIR / Resolution: 1.95→24 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.949 / SU B: 3.6 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19	7402	5 %	RANDOM
R_work	0.165	-	-	-
obs	0.166	140398	94.1 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Refinement step

Cycle: LAST / Resolution: 1.95→24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9520	0	72	1213	10805

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	9760
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9184
X-RAY DIFFRACTION	r_angle_refined_deg
X-RAY DIFFRACTION	r_angle_other_deg	1.799	1.987	13192
X-RAY DIFFRACTION	r_dihedral_angle_1_deg
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	1.117	3	21424
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	1520
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	10928
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1800
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.3	2119
X-RAY DIFFRACTION	r_nbd_other	0.21	0.3	8826
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.5	1016
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.208	0	7
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.153	0.3	32
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.178	0.3	153
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.125	0.5	64
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	0.674	1.5	6384
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.284	2	10184
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.667	3	3376
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.489	4.5	3008
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	880	tight positional	0.12	0.05
1	2	B	880	tight positional	0.11	0.05
1	3	C	880	tight positional	0.07	0.05
1	4	D	880	tight positional	0.08	0.05
1	5	E	880	tight positional	0.07	0.05
1	6	F	880	tight positional	0.07	0.05
1	7	G	880	tight positional	0.1	0.05
1	8	H	880	tight positional	0.08	0.05
2	1	A	894	tight positional	0.01	0.05
2	2	B	894	tight positional	0.01	0.05
2	3	C	894	tight positional	0.01	0.05
2	4	D	894	tight positional	0.01	0.05
2	5	E	894	tight positional	0.01	0.05
2	6	F	894	tight positional	0.01	0.05
2	7	G	894	tight positional	0.01	0.05
2	8	H	894	tight positional	0.01	0.05
1	1	A	57	medium positional	0.37	0.5
1	2	B	57	medium positional	1.01	0.5
1	3	C	57	medium positional	0.43	0.5
1	4	D	57	medium positional	0.42	0.5
1	5	E	57	medium positional	0.42	0.5
1	6	F	57	medium positional	0.43	0.5
1	7	G	57	medium positional	0.45	0.5
1	8	H	57	medium positional	1.4	0.5
2	1	A	57	medium positional	0.08	0.5
2	2	B	57	medium positional	0.13	0.5
2	3	C	57	medium positional	0.09	0.5
2	4	D	57	medium positional	0.09	0.5
2	5	E	57	medium positional	0.09	0.5
2	6	F	57	medium positional	0.09	0.5
2	7	G	57	medium positional	0.09	0.5
2	8	H	57	medium positional	0.16	0.5
1	1	A	1396	loose positional	0.65	5
1	2	B	1396	loose positional	0.78	5
1	3	C	1396	loose positional	0.47	5
1	4	D	1396	loose positional	0.49	5
1	5	E	1396	loose positional	0.58	5
1	6	F	1396	loose positional	0.49	5
1	7	G	1396	loose positional	0.7	5
1	8	H	1396	loose positional	0.89	5
2	1	A	1396	loose positional	0.02	5
2	2	B	1396	loose positional	0.02	5
2	3	C	1396	loose positional	0.02	5
2	4	D	1396	loose positional	0.02	5
2	5	E	1396	loose positional	0.02	5
2	6	F	1396	loose positional	0.02	5
2	7	G	1396	loose positional	0.02	5
2	8	H	1396	loose positional	0.03	5
1	1	A	880	tight thermal	0.21	0.5
1	2	B	880	tight thermal	0.2	0.5
1	3	C	880	tight thermal	0.2	0.5
1	4	D	880	tight thermal	0.2	0.5
1	5	E	880	tight thermal	0.19	0.5
1	6	F	880	tight thermal	0.17	0.5
1	7	G	880	tight thermal	0.18	0.5
1	8	H	880	tight thermal	0.18	0.5
2	1	A	894	tight thermal	1.22	0.5
2	2	B	894	tight thermal	1.18	0.5
2	3	C	894	tight thermal	1.18	0.5
2	4	D	894	tight thermal	1.19	0.5
2	5	E	894	tight thermal	1.15	0.5
2	6	F	894	tight thermal	1.09	0.5
2	7	G	894	tight thermal	1.13	0.5
2	8	H	894	tight thermal	1.11	0.5
1	1	A	57	medium thermal	1.75	2
1	2	B	57	medium thermal	4.94	2
1	3	C	57	medium thermal	0.81	2
1	4	D	57	medium thermal	2.86	2
1	5	E	57	medium thermal	1.53	2
1	6	F	57	medium thermal	2.23	2
1	7	G	57	medium thermal	1.86	2
1	8	H	57	medium thermal	4.43	2
2	1	A	57	medium thermal	13.84	2
2	2	B	57	medium thermal	23.25	2
2	3	C	57	medium thermal	9.43	2
2	4	D	57	medium thermal	17.67	2
2	5	E	57	medium thermal	12.95	2
2	6	F	57	medium thermal	15.62	2
2	7	G	57	medium thermal	14.27	2
2	8	H	57	medium thermal	22.01	2
1	1	A	1396	loose thermal	1.66	10
1	2	B	1396	loose thermal	2.17	10
1	3	C	1396	loose thermal	1.44	10
1	4	D	1396	loose thermal	1.63	10
1	5	E	1396	loose thermal	1.58	10
1	6	F	1396	loose thermal	1.31	10
1	7	G	1396	loose thermal	1.51	10
1	8	H	1396	loose thermal	1.78	10
2	1	A	1396	loose thermal	2.73	10
2	2	B	1396	loose thermal	3.11	10
2	3	C	1396	loose thermal	2.53	10
2	4	D	1396	loose thermal	2.7	10
2	5	E	1396	loose thermal	2.66	10
2	6	F	1396	loose thermal	2.42	10
2	7	G	1396	loose thermal	2.6	10
2	8	H	1396	loose thermal	2.82	10

LS refinement shell

Resolution: 1.95→2 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.237	551
R_work	0.2	10293

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	2.0339	-0.0882	0.3877	0.9453	-0.5139	2.3691	-0.0279	0.1243	0.1811	-0.1246	0.0096	0.0595	-0.1723	-0.3316	0.0183	0.0598	0.0084	-0.0031	0.1344	-0.0068	0.0603	-6.331	6.758	-26.961
2	1.2985	-0.4076	-0.3371	2.7278	2.1782	3.4199	-0.0033	0.3506	-0.0708	-0.216	-0.2676	0.2619	0.0377	-0.2567	0.2709	0.062	0.0335	-0.0013	0.1738	-0.0434	0.0854	-8.855	23	5.726
3	1.7155	0.0644	-0.9259	1.3897	0.1812	2.1905	-0.1284	0.2403	-0.2124	-0.182	-0.0509	0.0374	0.2087	-0.0479	0.1793	0.0959	-0.0254	0.0532	0.0182	-0.0369	0.0749	-24.825	18.603	36.732
4	1.2767	0.2821	-0.8021	2.0637	-0.996	2.057	-0.0563	0.0145	-0.0538	-0.1583	-0.1025	-0.2789	-0.0361	0.281	0.1588	0.0653	0.0027	0.0398	0.0382	0.0287	0.0825	-23.644	1.087	67.518
5	2.8511	-1.1434	1.2402	2.4724	-0.361	2.0086	0.0337	0.4936	0.2936	-0.4055	-0.2862	-0.0965	-0.1675	0.0773	0.2525	0.1602	0.0054	-0.0492	0.1167	0.0517	0.1211	58.443	2.899	-26.266
6	1.7316	0.51	0.5145	2.0273	0.7604	1.7197	-0.0655	0.1165	0.062	-0.2067	-0.0092	0.2401	0.0622	-0.144	0.0747	0.1002	0.0019	-0.0624	0.0461	-0.0071	0.1184	56.277	20.312	4.676
7	1.8236	-0.3014	-0.7862	1.7206	0.3822	1.8468	-0.0037	0.0839	-0.1418	-0.249	0.0104	-0.0426	0.2692	0.0586	-0.0067	0.1519	-0.0341	-0.013	0.1392	-0.0065	0.0741	38.147	19.966	35.267
8	1.5734	-0.0821	-0.0643	2.4085	-1.5129	3.0266	0.0099	0.3282	0.0104	-0.3448	-0.0952	-0.1411	0.0799	0.2207	0.0853	0.0924	0.0575	0.0099	0.2385	0.0063	0.0744	41.824	3.55	67.978

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 161
2	X-RAY DIFFRACTION	1	A	1162
3	X-RAY DIFFRACTION	2	B	1 - 161
4	X-RAY DIFFRACTION	2	B	1162
5	X-RAY DIFFRACTION	3	C	1 - 161
6	X-RAY DIFFRACTION	3	C	1162
7	X-RAY DIFFRACTION	4	D	1 - 161
8	X-RAY DIFFRACTION	4	D	1162
9	X-RAY DIFFRACTION	5	E	1 - 161
10	X-RAY DIFFRACTION	5	E	1162
11	X-RAY DIFFRACTION	6	F	1 - 161
12	X-RAY DIFFRACTION	6	F	1162
13	X-RAY DIFFRACTION	7	G	1 - 161
14	X-RAY DIFFRACTION	7	G	1162
15	X-RAY DIFFRACTION	8	H	1 - 161
16	X-RAY DIFFRACTION	8	H	1162

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Assembly

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Experiment

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About Yorodumi

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

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Yorodumi