PDB-7e4u: Crystal structure of Peroxiredoxin-1

ID or keywords:

Entry

Database: PDB / ID: 7e4u

Title

Crystal structure of Peroxiredoxin-1

Components

Peroxiredoxin 1

Keywords

OXIDOREDUCTASE / Peroxidase

Function / homology

Function and homology information

peroxiredoxin activity / peroxidase activity
Similarity search - Function

Biological species

Sparus aurata (gilthead seabream)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Ahmed, S. / Mok, Y.K. / Jobichen, C.

Citation

Journal: To Be Published
Title: Crystal structure of Peroxiredoxin-1
Authors: Ahmed, S. / Mok, Y.K. / Jobichen, C.

History

Deposition	Feb 15, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7e4u.cif.gz	344.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7e4u.ent.gz	280.7 KB	Display	PDB format
PDBx/mmJSON format	7e4u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7e4u_validation.pdf.gz	522.5 KB	Display	wwPDB validaton report
Full document	7e4u_full_validation.pdf.gz	541.3 KB	Display
Data in XML	7e4u_validation.xml.gz	61.8 KB	Display
Data in CIF	7e4u_validation.cif.gz	84.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e4/7e4u ftp://data.pdbj.org/pub/pdb/validation_reports/e4/7e4u	HTTPS FTP

-
Related structure data

Related structure data	4xcsS S: Starting model for refinement
Similar structure data	4xcs-1 7e4u-2 7e4u-4 7e4u-5 7e4u-3 2ozt-d 6yze-d 4xcs-2 5eks-1 2wdt-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) 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

4xcsS

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Peroxiredoxin 1

B: Peroxiredoxin 1

C: Peroxiredoxin 1

D: Peroxiredoxin 1

E: Peroxiredoxin 1

F: Peroxiredoxin 1

G: Peroxiredoxin 1

H: Peroxiredoxin 1

I: Peroxiredoxin 1

J: Peroxiredoxin 1

hetero molecules

221 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Peroxiredoxin 1

B: Peroxiredoxin 1

hetero molecules

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

2

C: Peroxiredoxin 1

D: Peroxiredoxin 1

hetero molecules

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

3

E: Peroxiredoxin 1

F: Peroxiredoxin 1

hetero molecules

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

4

G: Peroxiredoxin 1

H: Peroxiredoxin 1

hetero molecules

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

5

I: Peroxiredoxin 1

J: Peroxiredoxin 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	217.452, 60.606, 205.142
Angle α, β, γ (deg.)	90.000, 94.230, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	3 - 172
2	1	1	1	B	3 - 172
1	1	2	1	A	3 - 172
2	1	2	1	C	3 - 172
1	1	3	1	A	3 - 173
2	1	3	1	D	3 - 173
1	1	4	1	A	3 - 171
2	1	4	1	E	3 - 171
1	1	5	1	A	3 - 178
2	1	5	1	F	3 - 178
1	1	6	1	A	3 - 170
2	1	6	1	G	3 - 170
1	1	7	1	A	3 - 174
2	1	7	1	H	3 - 174
1	1	8	1	A	3 - 173
2	1	8	1	I	3 - 173
1	1	9	1	A	3 - 173
2	1	9	1	J	3 - 173
1	1	10	1	B	3 - 173
2	1	10	1	C	3 - 173
1	1	11	1	B	3 - 172
2	1	11	1	D	3 - 172
1	1	12	1	B	3 - 171
2	1	12	1	E	3 - 171
1	1	13	1	B	3 - 172
2	1	13	1	F	3 - 172
1	1	14	1	B	3 - 170
2	1	14	1	G	3 - 170
1	1	15	1	B	3 - 172
2	1	15	1	H	3 - 172
1	1	16	1	B	3 - 172
2	1	16	1	I	3 - 172
1	1	17	1	B	3 - 172
2	1	17	1	J	3 - 172
1	1	18	1	C	3 - 172
2	1	18	1	D	3 - 172
1	1	19	1	C	3 - 171
2	1	19	1	E	3 - 171
1	1	20	1	C	3 - 172
2	1	20	1	F	3 - 172
1	1	21	1	C	3 - 170
2	1	21	1	G	3 - 170
1	1	22	1	C	3 - 172
2	1	22	1	H	3 - 172
1	1	23	1	C	3 - 172
2	1	23	1	I	3 - 172
1	1	24	1	C	3 - 172
2	1	24	1	J	3 - 172
1	1	25	1	D	3 - 171
2	1	25	1	E	3 - 171
1	1	26	1	D	3 - 173
2	1	26	1	F	3 - 173
1	1	27	1	D	3 - 170
2	1	27	1	G	3 - 170
1	1	28	1	D	3 - 173
2	1	28	1	H	3 - 173
1	1	29	1	D	3 - 174
2	1	29	1	I	3 - 174
1	1	30	1	D	3 - 174
2	1	30	1	J	3 - 174
1	1	31	1	E	3 - 171
2	1	31	1	F	3 - 171
1	1	32	1	E	3 - 170
2	1	32	1	G	3 - 170
1	1	33	1	E	3 - 171
2	1	33	1	H	3 - 171
1	1	34	1	E	3 - 171
2	1	34	1	I	3 - 171
1	1	35	1	E	3 - 171
2	1	35	1	J	3 - 171
1	1	36	1	F	3 - 170
2	1	36	1	G	3 - 170
1	1	37	1	F	3 - 174
2	1	37	1	H	3 - 174
1	1	38	1	F	3 - 173
2	1	38	1	I	3 - 173
1	1	39	1	F	3 - 173
2	1	39	1	J	3 - 173
1	1	40	1	G	3 - 170
2	1	40	1	H	3 - 170
1	1	41	1	G	3 - 170
2	1	41	1	I	3 - 170
1	1	42	1	G	3 - 170
2	1	42	1	J	3 - 170
1	1	43	1	H	3 - 173
2	1	43	1	I	3 - 173
1	1	44	1	H	3 - 173
2	1	44	1	J	3 - 173
1	1	45	1	I	3 - 174
2	1	45	1	J	3 - 174

NCS ensembles :
NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.881153, 0.188251, 0.433741), (0.202253, -0.679109, 0.705624), (0.427392, 0.709488, 0.560324)	81.857941, -11.00019, -17.737261

#1: Protein	Peroxiredoxin 1 Mass: 22025.180 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sparus aurata (gilthead seabream) / Gene: PRDX1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: G0T332
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.8 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 14.4% W/V PEG 8000, 0.08 M Sodium cacodylate, 0.16 M Calcium acetate hydrate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.98 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 9, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.6→49.49 Å / Num. obs: 79576 / % possible obs: 97.6 % / Redundancy: 4 % / R_sym value: 0.25 / Net I/σ(I): 3.4
Reflection shell	Resolution: 2.6→2.67 Å / R_merge(I) obs: 0.25 / Num. unique obs: 5176

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4XCS

4xcs

Resolution: 2.6→49.49 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.907 / SU B: 11.728 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.407 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.252	965	1.2 %	RANDOM
R_work	0.206	-	-	-
obs	0.206	79576	97.6 %	-

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 max: 143.16 Å² / B_iso mean: 50.86 Å² / B_iso min: 27.16 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	0 Å²	-0.03 Å²
2-	-	0.03 Å²	0 Å²
3-	-	-	0 Å²

Refinement step

Cycle: final / Resolution: 2.6→49.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13429	0	53	248	13730
B_iso mean	-	-	88.84	47.84	-
Num. residues	-	-	-	-	1722

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	13808
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	12949
X-RAY DIFFRACTION	r_angle_refined_deg	1.684	1.643	18658
X-RAY DIFFRACTION	r_angle_other_deg	1.285	1.586	29975
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.419	5	1714
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.422	22.238	697
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.457	15	2314
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.521	15	80
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1835
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	15418
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3018
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1338	TIGHT POSITIONAL	0.55	0.15
1	A	1332	TIGHT POSITIONAL	0.55	0.15
1	A	1327	TIGHT POSITIONAL	0.33	0.15
1	A	1332	TIGHT POSITIONAL	0.54	0.15
1	A	1318	TIGHT POSITIONAL	0.52	0.15
1	A	1328	TIGHT POSITIONAL	0.54	0.15
1	A	1314	TIGHT POSITIONAL	0.44	0.15
1	A	1332	TIGHT POSITIONAL	0.57	0.15
1	A	1334	TIGHT POSITIONAL	0.29	0.15
1	A	1327	TIGHT POSITIONAL	0.53	0.15
1	A	1328	TIGHT THERMAL	5.02	1.5
2	A	1334	TIGHT POSITIONAL	0.29	0.15
2	A	1318	TIGHT POSITIONAL	0.3	0.15
2	A	1328	TIGHT POSITIONAL	0.29	0.15
2	A	1314	TIGHT POSITIONAL	0.31	0.15
2	A	1334	TIGHT POSITIONAL	0.36	0.15
2	A	1327	TIGHT POSITIONAL	0.53	0.15
2	A	1340	TIGHT POSITIONAL	0.34	0.15
2	A	1318	TIGHT POSITIONAL	0.29	0.15
2	A	1334	TIGHT POSITIONAL	0.33	0.15
2	A	1325	TIGHT POSITIONAL	0.32	0.15
2	A	1330	TIGHT THERMAL	3.82	1.5
3	A	1345	TIGHT POSITIONAL	0.41	0.15
3	A	1327	TIGHT POSITIONAL	0.54	0.15
3	A	1318	TIGHT POSITIONAL	0.5	0.15
3	A	1323	TIGHT POSITIONAL	0.52	0.15
3	A	1309	TIGHT POSITIONAL	0.43	0.15
3	A	1327	TIGHT POSITIONAL	0.57	0.15
3	A	1318	TIGHT POSITIONAL	0.3	0.15
3	A	1341	TIGHT POSITIONAL	0.36	0.15
3	A	1320	TIGHT POSITIONAL	0.28	0.15
3	A	1340	TIGHT POSITIONAL	0.33	0.15
3	A	1336	TIGHT THERMAL	5.25	1.5
4	A	1318	TIGHT POSITIONAL	0.35	0.15
4	A	1304	TIGHT POSITIONAL	0.31	0.15
4	A	1318	TIGHT POSITIONAL	0.34	0.15
4	A	1320	TIGHT POSITIONAL	0.31	0.15
4	A	1334	TIGHT POSITIONAL	0.32	0.15
4	A	1325	TIGHT POSITIONAL	0.4	0.15
4	A	1323	TIGHT THERMAL	5.58	1.5
5	A	1371	TIGHT THERMAL	3.21	1.5
6	A	1314	TIGHT THERMAL	5.32	1.5
7	A	1337	TIGHT THERMAL	5.98	1.5
8	A	1316	TIGHT THERMAL	9.8	1.5
9	A	1336	TIGHT THERMAL	11.44	1.5
10	B	1338	TIGHT THERMAL	5.58	1.5
11	B	1332	TIGHT THERMAL	5.96	1.5
12	B	1327	TIGHT THERMAL	3.44	1.5
13	B	1332	TIGHT THERMAL	5.24	1.5
14	B	1318	TIGHT THERMAL	5.19	1.5
15	B	1328	TIGHT THERMAL	6.88	1.5
16	B	1314	TIGHT THERMAL	11.49	1.5
17	B	1332	TIGHT THERMAL	13.13	1.5
18	C	1334	TIGHT THERMAL	3.7	1.5
19	C	1327	TIGHT THERMAL	5.87	1.5
20	C	1334	TIGHT THERMAL	3.54	1.5
21	C	1318	TIGHT THERMAL	4.98	1.5
22	C	1328	TIGHT THERMAL	4.65	1.5
23	C	1314	TIGHT THERMAL	8.54	1.5
24	C	1334	TIGHT THERMAL	10.17	1.5
25	D	1327	TIGHT THERMAL	6.12	1.5
26	D	1340	TIGHT THERMAL	5.17	1.5
27	D	1318	TIGHT THERMAL	5.36	1.5
28	D	1334	TIGHT THERMAL	4.44	1.5
29	D	1325	TIGHT THERMAL	8.46	1.5
30	D	1345	TIGHT THERMAL	10.05	1.5
31	E	1327	TIGHT THERMAL	5.68	1.5
32	E	1318	TIGHT THERMAL	5.27	1.5
33	E	1323	TIGHT THERMAL	6.88	1.5
34	E	1309	TIGHT THERMAL	11.44	1.5
35	E	1327	TIGHT THERMAL	12.98	1.5
36	F	1318	TIGHT THERMAL	5.06	1.5
37	F	1341	TIGHT THERMAL	5.74	1.5
38	F	1320	TIGHT THERMAL	9.31	1.5
39	F	1340	TIGHT THERMAL	10.93	1.5
40	G	1318	TIGHT THERMAL	5.69	1.5
41	G	1304	TIGHT THERMAL	8.86	1.5
42	G	1318	TIGHT THERMAL	10.85	1.5
43	H	1320	TIGHT THERMAL	6.91	1.5
44	H	1334	TIGHT THERMAL	7.93	1.5
45	I	1325	TIGHT THERMAL	5.25	1.5

LS refinement shell

Resolution: 2.6→2.67 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.326	61	-
R_work	0.299	5170	-
all	-	5231	-
obs	-	-	86.14 %

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi