PDB-4kce: Crystal structure of the mitochondrial peroxiredoxin from Leishma...

ID or keywords:

Entry

Database: PDB / ID: 4kce

Title

Crystal structure of the mitochondrial peroxiredoxin from Leishmania braziliensis in the dimeric form

Components

Peroxidoxin

Keywords

OXIDOREDUCTASE / Thioredoxin-like

Function / homology

Function and homology information

thioredoxin-dependent peroxiredoxin / peroxiredoxin activity
Similarity search - Function

Biological species

Leishmania braziliensis (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.79 Å

Authors

Souza, T.A.C.B. / Morais, M.A.B. / Giuseppe, P.O. / Murakami, M.T.

Citation

Journal: To be Published
Title: Crystal structure of the mitochondrial peroxiredoxin from Leishmania braziliensis in the dimeric form
Authors: Souza, T.A.C.B. / Morais, M.A.B. / Giuseppe, P.O. / Murakami, M.T.

History

Deposition	Apr 24, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 14, 2014	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4kce.cif.gz	141 KB	Display	PDBx/mmCIF format
PDB format	pdb4kce.ent.gz	118.2 KB	Display	PDB format
PDBx/mmJSON format	4kce.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4kce_validation.pdf.gz	438.8 KB	Display	wwPDB validaton report
Full document	4kce_full_validation.pdf.gz	442.3 KB	Display
Data in XML	4kce_validation.xml.gz	13.5 KB	Display
Data in CIF	4kce_validation.cif.gz	17.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kc/4kce ftp://data.pdbj.org/pub/pdb/validation_reports/kc/4kce	HTTPS FTP

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Related structure data

Related structure data	4kb3
Similar structure data	1qq2-d 6yky-3 2e9u-d 5i0p-2 4xcs-1 5i0p-3 4xcs-3 5opv-d 6i95-d 2c4k-1 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: Peroxidoxin

B: Peroxidoxin

47.4 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)	132.485, 132.485, 44.627
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2

#1: Protein	Peroxidoxin Mass: 23689.945 Da / Num. of mol.: 2 / Fragment: UNP residues 34-225 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania braziliensis (eukaryote) / Gene: LBRM_23_0050 / Production host: Escherichia coli (E. coli) References: UniProt: A4HCL7, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.48 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 27% PEG 4.000 (w/v), 0.1 M Tris-HCl pH 8.5 and 0.2 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

LNLS

/ Beamline: W01B-MX2 / Wavelength: 1.459 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2012

Radiation

Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.459 Å / Relative weight: 1

Reflection

Resolution: 2.79→40.2891 Å / Num. all: 10370 / Num. obs: 10240 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 80.087 Å² / R_merge(I) obs: 0.2 / Net I/σ(I): 10.58

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
2.79-2.96	0.032	0.85	18831	1506	1	92.9
2.96-3.16	0.032	2.03	21410	1527	1	99.9
3.16-3.41	0.032	3.84	20239	1441	1	100
3.41-3.74	0.032	7	18569	1332	1	100
3.74-4.17	0.032	11.14	16703	1203	1	99.9
4.17-4.81	0.032	19.01	14824	1084	1	99.7
4.81-5.87	0.032	19.44	12429	932	1	100
5.87-8.22	0.032	24.8	9610	747	1	100
8.22-40.289	0.032	39.34	5316	468	1	97.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
MOLREP		phasing
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.79→19.916 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.7743 / SU ML: 0.39 / σ(F): 2 / Phase error: 28.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2784	888	8.71 %	RANDOM
R_work	0.2385	-	-	-
obs	0.2418	10200	98.75 %	-
all	-	11088	-	-

Solvent computation

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

Displacement parameters

B_iso max: 141.2 Å² / B_iso mean: 53.9531 Å² / B_iso min: 22.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.79→19.916 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2592	0	0	0	2592

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2645
X-RAY DIFFRACTION	f_angle_d	1.069	3580
X-RAY DIFFRACTION	f_chiral_restr	0.068	402
X-RAY DIFFRACTION	f_plane_restr	0.006	462
X-RAY DIFFRACTION	f_dihedral_angle_d	12.142	974

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.7904-2.9647	0.3536	128	0.3493	1430	1558	93
2.9647-3.1927	0.3716	168	0.3043	1515	1683	100
3.1927-3.5124	0.3472	250	0.2501	1426	1676	100
3.5124-4.0171	0.3017	137	0.2168	1583	1720	100
4.0171-5.0474	0.2504	98	0.1947	1629	1727	100
5.0474-19.9162	0.2207	107	0.244	1729	1836	100

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	2.1169	0.5768	-0.6372	0.6678	0.0419	0.8495	-0.2088	0.1927	-0.1809	-0.0151	0.0652	-0.0864	0.1229	-0.2245	-0.0283	0.1533	-0.2501	0.0912	0.7267	0.3655	1.7912	4.2889	-48.0434	-5.2711
2	4.1093	0.1175	-1.4745	0.3411	0.6167	1.957	-1.5851	-1.3362	-1.8807	1.0661	0.6087	-0.3388	1.0576	0.1286	0.5344	0.7458	0.2554	0.184	0.571	0.1277	0.8127	24.522	-49.24	-5.1689
3	5.1109	2.2562	0.544	7.5311	1.5798	5.0017	-0.0467	0.703	1.1668	-0.4769	-0.3221	0.7748	-0.5414	-0.0181	0.4082	0.278	0.0426	-0.0183	0.4143	0.1109	0.4866	22.4603	-34.7732	-12.1137
4	2.3993	-1.3862	-0.5493	2.953	0.9623	2.8085	-0.3297	-0.7387	0.2289	0.2799	0.6424	-0.2653	0.2951	1.2769	0.0031	0.3043	-0.0127	-0.0609	0.4651	0.0798	0.234	24.8544	-39.9094	-5.9339
5	6.3636	-0.0072	0.0418	0.5164	-0.8006	1.2454	0.1067	0.4633	-0.2594	-0.6044	0.0176	0.241	0.0463	0.0347	0.0449	0.2662	0.1675	0.041	0.3072	-0.2187	0.722	32.8784	-40.5324	-17.3117
6	5.026	2.3253	-1.8278	5.3207	-1.1273	2.7736	0.056	0.9322	-0.17	0.1142	0.3134	-0.0358	-0.0727	-0.3051	-0.1575	0.2251	0.1363	0.0168	0.4023	0.02	0.469	32.0176	-36.3253	-13.3262
7	1.6716	-0.3975	-1.0304	1.1999	-0.3301	1.4236	0.0018	1.3463	-0.5318	-0.1391	-0.0803	-0.2797	0.6254	0.619	0.0132	0.3888	-0.1421	0.021	1.1809	-0.3974	0.8582	14.7632	-48.395	-19.6178
8	2.1179	-0.4004	1.3376	1.4446	0.3794	2.973	0.578	0.2808	-0.1624	-0.0556	-0.0319	-0.3452	0.4638	-0.1881	0.179	-0.1808	0.3674	-0.0038	0.5489	-0.1683	0.4221	11.8494	-41.2501	-9.4167
9	0.6554	0.8178	0.523	3.0993	-0.8932	1.5713	0.174	0.5009	0.9858	0.5168	-0.317	0.3474	-1.0123	-0.9448	0.1228	0.2864	0.1451	0.0822	0.5044	0.0167	0.3981	14.1429	-30.6739	-8.2192
10	0.7521	0.622	-0.2166	0.6169	-0.3355	6.3037	0.1282	-0.4786	-0.0261	0.2851	-0.0641	0.0275	0.3037	-0.3183	-0.0294	0.5025	0.2006	0.1074	0.7672	0.1397	0.2878	11.4458	-36.0824	4.1163
11	4.0974	-0.0961	-2.6799	6.3388	5.6639	6.7091	0.051	0.0229	0.0059	0.0671	-0.6728	0.4611	-0.2199	-1.9656	0.3419	1.0404	0.3653	0.1136	1.3695	0.1671	0.2133	5.9264	-37.4525	10.1209
12	3.2542	-0.5455	-2.4993	0.6169	0.2233	3.5084	0.4398	0.3524	-0.1318	0.0623	0.2416	-0.1084	0.5576	-0.2133	0.9473	0.189	0.1398	0.0854	0.8602	-0.4739	0.174	-7.0445	-34.126	-18.8082
13	1.6146	0.1583	1.9723	1.4981	0.4687	2.4772	0.1594	1.4937	-0.1248	-0.5208	-0.0488	-0.235	-0.1491	0.7744	-0.0009	0.4052	-0.1548	-0.5554	1.4804	0.3156	1.0431	-14.3086	-27.6524	-19.2843
14	3.3261	-0.5092	1.4606	3.6739	2.2542	3.1746	-0.1836	-0.5578	-0.7415	0.7386	-0.1112	0.5353	1.0486	0.028	-0.0352	0.2977	0.0947	0.0121	0.4715	0.1712	0.3679	-5.0363	-31.986	-4.9773
15	6.9261	-0.0749	-3.0905	3.972	1.5029	2.7847	-0.3628	0.1052	1.2621	0.175	-0.2197	-0.1984	-1.5912	-0.4765	0.5864	0.4736	0.0914	-0.1318	0.344	0.0131	0.8663	-3.0528	-20.3395	-7.0117
16	1.463	-0.1097	0.6175	1.7593	0.4879	1.1073	-0.0851	0.4487	0.6047	0.1679	-0.405	0.0147	0.1439	-0.2864	0.0966	-0.0677	0.0942	0.4467	0.7927	0.2396	0.407	-8.4583	-27.4973	-11.8098
17	1.7969	-0.6731	-0.8053	1.362	-1.6896	3.9184	-0.526	0.0581	-0.5845	0.1735	0.4955	-0.1742	0.143	-0.3322	0.0243	0.2759	-0.0033	0.0633	0.3124	-0.0182	0.8622	-18.8234	-29.671	-3.3028
18	3.5769	-0.1306	-1.7016	2.6883	-0.561	1.5085	0.9322	-0.4025	0.2602	0.5876	-0.556	-0.3379	-0.3111	0.1402	-0.2349	0.4541	-0.2136	0.0979	0.9312	0.1057	0.6356	-15.1373	-23.3818	5.6188
19	2.408	-1.4262	-0.1656	3.7727	2.3135	3.9721	0.2002	0.4656	-0.0723	0.406	-0.6137	0.376	0.7937	-0.3794	0.4218	0.2918	-0.0309	0.0387	0.5096	-0.0792	0.5937	-9.4938	-37.3301	-8.5338
20	0.9454	0.5669	-0.0829	0.7486	-0.0719	0.3468	0.3944	-0.2797	0.5599	-0.0445	-0.4295	0.1445	-0.3045	-0.3284	-0.322	-0.1944	-0.0618	0.3516	0.7942	0.4009	0.1947	0.0652	-31.4165	-16.9118
21	1.8263	0.8876	0.3971	3.9077	0.4868	1.6333	-0.3852	0.3341	-0.1455	0.0628	0.5521	0.1783	-0.2732	0.469	-0.1681	0.2476	0.0563	0.017	0.6393	0.1118	0.603	3.956	-31.9743	-9.101
22	5.7074	-3.0747	-1.1159	9.7568	1.1993	3.6365	0.0006	1.5894	1.2845	-1.4454	-0.8631	-0.2367	-0.3792	-0.5168	0.2542	0.2146	0.0864	0.0361	0.5399	0.2553	0.9361	9.3851	-22.9298	-20.6807

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 36:41)	A	36 - 41
2	X-RAY DIFFRACTION	2	(chain A and resid 42:67)	A	42 - 67
3	X-RAY DIFFRACTION	3	(chain A and resid 68:91)	A	68 - 91
4	X-RAY DIFFRACTION	4	(chain A and resid 92:111)	A	92 - 111
5	X-RAY DIFFRACTION	5	(chain A and resid 112:117)	A	112 - 117
6	X-RAY DIFFRACTION	6	(chain A and resid 118:136)	A	118 - 136
7	X-RAY DIFFRACTION	7	(chain A and resid 137:151)	A	137 - 151
8	X-RAY DIFFRACTION	8	(chain A and resid 152:175)	A	152 - 175
9	X-RAY DIFFRACTION	9	(chain A and resid 176:188)	A	176 - 188
10	X-RAY DIFFRACTION	10	(chain A and resid 189:193)	A	189 - 193
11	X-RAY DIFFRACTION	11	(chain A and resid 194:203)	A	194 - 203
12	X-RAY DIFFRACTION	12	(chain B and resid 36:52)	B	36 - 52
13	X-RAY DIFFRACTION	13	(chain B and resid 53:64)	B	53 - 64
14	X-RAY DIFFRACTION	14	(chain B and resid 65:83)	B	65 - 83
15	X-RAY DIFFRACTION	15	(chain B and resid 84:96)	B	84 - 96
16	X-RAY DIFFRACTION	16	(chain B and resid 97:110)	B	97 - 110
17	X-RAY DIFFRACTION	17	(chain B and resid 111:117)	B	111 - 117
18	X-RAY DIFFRACTION	18	(chain B and resid 118:125)	B	118 - 125
19	X-RAY DIFFRACTION	19	(chain B and resid 126:156)	B	126 - 156
20	X-RAY DIFFRACTION	20	(chain B and resid 157:165)	B	157 - 165
21	X-RAY DIFFRACTION	21	(chain B and resid 166:186)	B	166 - 186
22	X-RAY DIFFRACTION	22	(chain B and resid 187:198)	B	187 - 198

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