PDB-4llr: Tryparedoxin peroxidase (TXNPX) from trypanosoma cruzi in the red...

Basic information

• Entry: Database: PDB / ID: 4llr
• Title: Tryparedoxin peroxidase (TXNPX) from trypanosoma cruzi in the reduced state
• Components: Tryparedoxin peroxidase
• Keywords: OXIDOREDUCTASE / PEROXIREDOXIN / PEROXIDASE

Function / homology

Function:

thioredoxin peroxidase activity / cellular response to stress / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol

Domain/homology:

Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta

Component:

Tryparedoxin peroxidase

• Biological species: Trypanosoma cruzi (eukaryote)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
• Authors: Pineyro, M.D. / Pizarro, J.C. / Lema, F. / Pritsch, O. / Cayota, A. / Bentley, G.A. / Robello, C.
• Citation: Journal: J.STRUCT.BIOL. / Year: 2005; Title: Crystal structure of the TRYPAREDOXIN PEROXIDASE from the human parasite TRYPANOSOMA CRUZI; Authors: Pineyro, M.D. / Pizarro, J.C. / Lema, F. / Pritsch, O. / Cayota, A. / Bentley, G.A. / Robello, C.

History

Deposition	Jul 9, 2013	Deposition site: RCSB / Processing site: RCSB
Supersession	Oct 9, 2013	ID: 1UUL
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: 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 / _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

Assembly

Deposited unit

A: Tryparedoxin peroxidase

B: Tryparedoxin peroxidase

C: Tryparedoxin peroxidase

D: Tryparedoxin peroxidase

E: Tryparedoxin peroxidase

F: Tryparedoxin peroxidase

G: Tryparedoxin peroxidase

H: Tryparedoxin peroxidase

I: Tryparedoxin peroxidase

J: Tryparedoxin peroxidase

Summary:

• 223 kDa, 10 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	222,627	10
Polymers	222,627	10
Non-polymers	0	0
Water	8,161	453

1

Summary:

• Idetical with deposited unit
• defined by author&software

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	28280 Å2
ΔGint	-185 kcal/mol
Surface area	71350 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	125.555, 87.018, 127.144
Angle α, β, γ (deg.)	90.00, 102.77, 90.00
Int Tables number	4
Space group name H-M	P1211

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 4 - 197 / Label seq-ID: 4 - 197

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

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

Components

#1: Protein

A B C D E F G H I J
Tryparedoxin peroxidase / Tryparedoxin peroxidase homologue

Details:

Mass: 22262.688 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL BRENER / Gene: Tryp / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: O96763

#2: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.09 ų/Da / Density % sol: 60.16 %
• Crystal grow: Method: vapor diffusion, hanging drop / pH: 7.5 ; Details: 100MM EDTA, 15% PEG3350, 10% GLYCEROL, 100MM TRISHCL PH7.5, 100MM DTT, 0.25% DMSO, VAPOR DIFFUSION, HANGING DROP

Data collection

• Diffraction: Mean temperature: 287 K
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.933 Å
• Detector: Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 15, 2002
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.933 Å / Relative weight: 1
• Reflection: Resolution: 2.8→30 Å / Num. all: 66025 / Num. obs: 66025 / % possible obs: 99.9 % / Redundancy: 3.72 % / R_merge(I) obs: 0.132
• Reflection shell: Resolution: 2.8→2.87 Å / Redundancy: 3.63 % / R_merge(I) obs: 0.21 / Mean I/σ(I) obs: 6.44 / % possible all: 99.7

Phasing

• Phasing: Method: molecular replacement

Processing

Software

Name	Version	Classification	NB
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing
REFMAC	5.7.0032	refinement
PDB_EXTRACT	3.11	data extraction
ADSC	Quantum	data collection

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E2Y

1e2y

Resolution: 2.8→29.97 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.056 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.19518	3350	5.1 %	RANDOM
Rwork	0.16195	-	-	-
obs	0.16361	62685	99.81 %	-
all	-	62685	-	-

• 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 mean: 30.852 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.01 Å2	0 Å2	-0.14 Å2
2-	-	0.15 Å2	0 Å2
3-	-	-	-0.1 Å2

Refinement step

Cycle: LAST / Resolution: 2.8→29.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15380	0	0	453	15833

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	15760
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	15010
X-RAY DIFFRACTION	r_angle_refined_deg	1.83	1.969	21270
X-RAY DIFFRACTION	r_angle_other_deg	1.695	3	34810
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.619	5	1930
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.839	24.571	700
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.56	15	2810
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.286	15	70
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	2260
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	17580
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	3470
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_mcbond_it	2.268	2.833	7750
X-RAY DIFFRACTION	r_mcbond_other	2.268	2.832	7749
X-RAY DIFFRACTION	r_mcangle_it	3.606	4.237	9670
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.463	3.225	8010
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	11577	0.09
1	2	B	11577	0.09
2	1	A	11587	0.1
2	2	C	11587	0.1
3	1	A	11527	0.1
3	2	D	11527	0.1
4	1	A	11567	0.1
4	2	E	11567	0.1
5	1	A	11706	0.1
5	2	F	11706	0.1
6	1	A	11488	0.1
6	2	G	11488	0.1
7	1	A	11586	0.1
7	2	H	11586	0.1
8	1	A	11401	0.11
8	2	I	11401	0.11
9	1	A	11723	0.1
9	2	J	11723	0.1
10	1	B	11722	0.08
10	2	C	11722	0.08
11	1	B	11729	0.08
11	2	D	11729	0.08
12	1	B	11918	0.06
12	2	E	11918	0.06
13	1	B	11643	0.08
13	2	F	11643	0.08
14	1	B	11769	0.07
14	2	G	11769	0.07
15	1	B	11742	0.09
15	2	H	11742	0.09
16	1	B	11661	0.09
16	2	I	11661	0.09
17	1	B	11734	0.08
17	2	J	11734	0.08
18	1	C	11710	0.09
18	2	D	11710	0.09
19	1	C	11674	0.09
19	2	E	11674	0.09
20	1	C	11676	0.1
20	2	F	11676	0.1
21	1	C	11686	0.09
21	2	G	11686	0.09
22	1	C	11638	0.09
22	2	H	11638	0.09
23	1	C	11659	0.09
23	2	I	11659	0.09
24	1	C	11685	0.1
24	2	J	11685	0.1
25	1	D	11696	0.08
25	2	E	11696	0.08
26	1	D	11585	0.09
26	2	F	11585	0.09
27	1	D	11704	0.08
27	2	G	11704	0.08
28	1	D	11651	0.09
28	2	H	11651	0.09
29	1	D	11555	0.1
29	2	I	11555	0.1
30	1	D	11635	0.09
30	2	J	11635	0.09
31	1	E	11597	0.09
31	2	F	11597	0.09
32	1	E	11729	0.08
32	2	G	11729	0.08
33	1	E	11731	0.09
33	2	H	11731	0.09
34	1	E	11689	0.09
34	2	I	11689	0.09
35	1	E	11734	0.09
35	2	J	11734	0.09
36	1	F	11570	0.09
36	2	G	11570	0.09
37	1	F	11565	0.09
37	2	H	11565	0.09
38	1	F	11475	0.1
38	2	I	11475	0.1
39	1	F	11761	0.09
39	2	J	11761	0.09
40	1	G	11604	0.1
40	2	H	11604	0.1
41	1	G	11484	0.1
41	2	I	11484	0.1
42	1	G	11661	0.08
42	2	J	11661	0.08
43	1	H	11639	0.1
43	2	I	11639	0.1
44	1	H	11649	0.09
44	2	J	11649	0.09
45	1	I	11523	0.1
45	2	J	11523	0.1

LS refinement shell

Resolution: 2.8→2.872 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.301	240	-
Rwork	0.236	4521	-
obs	-	-	99.6 %