PDB-4cab: The refined structure of catalase DR1998 from Deinococcus radiodu...

ID or keywords:

Entry

Database: PDB / ID: 4cab

Title

The refined structure of catalase DR1998 from Deinococcus radiodurans at 2.6 A resolution

Components

CATALASE

Keywords

OXIDOREDUCTASE / HEME-CONTAINING CATALASE

Function / homology

Function and homology information

catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / heme binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

DEINOCOCCUS RADIODURANS R1 (radioresistant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.599 Å

Authors

Borges, P.T. / Miranda, C.S. / Santos, S.P. / Frazao, C. / Romao, C.V.

Citation

Journal: FEBS J. / Year: 2014
Title: Structure of the Mono-Functional Heme Catalase Dr1998 from Deinococcus Radiodurans
Authors: Borges, P.T. / Frazao, C. / Miranda, C.S. / Carrondo, M.A. / Romao, C.V.

History

Deposition	Oct 8, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	Aug 12, 2015	Group: Database references
Revision 1.2	Feb 27, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4cab.cif.gz	806 KB	Display	PDBx/mmCIF format
PDB format	pdb4cab.ent.gz	676 KB	Display	PDB format
PDBx/mmJSON format	4cab.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4cab_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	4cab_full_validation.pdf.gz	1.7 MB	Display
Data in XML	4cab_validation.xml.gz	74.4 KB	Display
Data in CIF	4cab_validation.cif.gz	100.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ca/4cab ftp://data.pdbj.org/pub/pdb/validation_reports/ca/4cab	HTTPS FTP

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Related structure data

Related structure data	1dgfS 1gweS 1m7sS 1sy7S 2iufS 2j2mS S: Starting model for refinement
Similar structure data	2a9e-1 2iqf-1 1mqf-1 1h7k-1 4qom-d 1qwl-1 1e93-1 1gwe-1 4blc-d 1qwm-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) 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	#57 - Sep 2004 Catalase similarity (12)

Deposited unit

A: CATALASE

B: CATALASE

C: CATALASE

D: CATALASE

hetero molecules

245 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CATALASE

B: CATALASE

hetero molecules

A: CATALASE

B: CATALASE

hetero molecules

defined by author&software
245 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: CATALASE

D: CATALASE

hetero molecules

C: CATALASE

D: CATALASE

hetero molecules

defined by author&software
245 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	97.326, 311.875, 145.628
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-2033- HOH
2	1	C-2019- HOH

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.9771, 0.001473, 0.2126), (0.002362, -1, 0.00393), (0.2126, 0.004343, -0.9771)	-5.596, 107.2, 51.09
2	given	(0.1074, -0.9942, -0.004396), (0.0632, 0.002417, 0.998), (-0.9922, -0.1075, 0.0631)	221.5, 10.76, 145.3
3	given	(0.1058, 0.9943, -0.009997), (-0.07404, -0.002149, -0.9973), (-0.9916, 0.1062, 0.07339)	-47.08, 97.39, 115.9

#1: Protein	CATALASE / CATALASE DR1998 Mass: 60588.977 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) DEINOCOCCUS RADIODURANS R1 (radioresistant) References: UniProt: Q59337, catalase
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.2 % / Description: NONE
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED AT 298K, FROM 0.2M MAGNESIUM ACETATE, 0.1 NA-CACODYLATE PH 6.5 AND 20% PEG 8000.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.82656
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2012 / Details: TOROIDAL MIRROR
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.82656 Å / Relative weight: 1
Reflection	Resolution: 2.6→49.4 Å / Num. obs: 68047 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / R_merge(I) obs: 0.31 / Net I/σ(I): 5.34
Reflection shell	Resolution: 2.6→2.76 Å / Redundancy: 4.57 % / R_merge(I) obs: 0.84 / Mean I/σ(I) obs: 1.7 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: LOOPS TRUNCATE ENSEMBLE OF PDB ENTRIES 2J2M, 1GWE, 2IUF, 1DGF, 1SY7, 1M7S

Resolution: 2.599→49.402 Å / SU ML: 0.3 / σ(F): 1704.59 / Phase error: 24.02 / Stereochemistry target values: ML
Details: CONVERGED TO R-WORK AND R-FREE OF 0.2224 A RESPECTIVELY USING A THIN-SHELLS R-FREE SET WITH 3762 REFLECTIONS

	R_factor	Num. reflection	% reflection
R_free	0.2363	-	-
R_work	0.2363	-	-
obs	0.2363	68012	97.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.599→49.402 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16296	0	182	554	17032

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	16935
X-RAY DIFFRACTION	f_angle_d	0.663	23014
X-RAY DIFFRACTION	f_dihedral_angle_d	11.344	6262
X-RAY DIFFRACTION	f_chiral_restr	0.024	2317
X-RAY DIFFRACTION	f_plane_restr	0.003	3101

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 (%)
2.5993-2.6288	0.3479	3848	0.3479	3848	X-RAY DIFFRACTION	87
2.6288-2.6598	0.3349	4127	0.3349	4127	X-RAY DIFFRACTION	95
2.6598-2.6922	0.3322	4319	0.3322	4319	X-RAY DIFFRACTION	97
2.6922-2.7263	0.3122	4272	0.3122	4272	X-RAY DIFFRACTION	98
2.7263-2.7621	0.3061	4302	0.3061	4302	X-RAY DIFFRACTION	98
2.7621-2.8	0.2973	4344	0.2973	4344	X-RAY DIFFRACTION	99
2.8-2.84	0.2969	4378	0.2969	4378	X-RAY DIFFRACTION	99
2.84-2.8824	0.3002	4313	0.3002	4313	X-RAY DIFFRACTION	99
2.8824-2.9274	0.291	4332	0.291	4332	X-RAY DIFFRACTION	99
2.9274-2.9754	0.2878	4341	0.2878	4341	X-RAY DIFFRACTION	99
2.9754-3.0267	0.2865	4346	0.2865	4346	X-RAY DIFFRACTION	99
3.0267-3.0817	0.2815	4352	0.2815	4352	X-RAY DIFFRACTION	99
3.0817-3.141	0.2769	4348	0.2769	4348	X-RAY DIFFRACTION	98
3.141-3.2051	0.2729	4264	0.2729	4264	X-RAY DIFFRACTION	99
3.2051-3.2748	0.2597	4362	0.2597	4362	X-RAY DIFFRACTION	99
3.2748-3.3509	0.2529	4304	0.2529	4304	X-RAY DIFFRACTION	98
3.3509-3.4347	0.249	4355	0.249	4355	X-RAY DIFFRACTION	99
3.4347-3.5275	0.2317	4312	0.2317	4312	X-RAY DIFFRACTION	99
3.5275-3.6313	0.2191	4346	0.2191	4346	X-RAY DIFFRACTION	98
3.6313-3.7485	0.2095	4320	0.2095	4320	X-RAY DIFFRACTION	98
3.7485-3.8824	0.2	4300	0.2	4300	X-RAY DIFFRACTION	98
3.8824-4.0378	0.2004	4302	0.2004	4302	X-RAY DIFFRACTION	98
4.0378-4.2215	0.1939	4323	0.1939	4323	X-RAY DIFFRACTION	98
4.2215-4.4439	0.1789	4305	0.1789	4305	X-RAY DIFFRACTION	98
4.4439-4.7221	0.1772	4340	0.1772	4340	X-RAY DIFFRACTION	99
4.7221-5.0864	0.182	4340	0.182	4340	X-RAY DIFFRACTION	98
5.0864-5.5976	0.1854	4318	0.1854	4318	X-RAY DIFFRACTION	99
5.5976-6.4061	0.1977	4338	0.1977	4338	X-RAY DIFFRACTION	99
6.4061-8.0653	0.1919	4334	0.1919	4334	X-RAY DIFFRACTION	98
8.0653-49.4104	0.1861	4320	0.1861	4320	X-RAY DIFFRACTION	98

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	0.4434	-0.0939	-0.164	0.5455	0.2355	0.7182	0.0837	-0.042	-0.0007	0.1542	-0.0232	0.2221	0.0102	-0.1323	0.0924	0.2079	-0.0437	0.001	0.1772	0.0114	0.249	78.3103	63.4494	48.1299
2	1.1873	0.186	-0.0209	0.5159	0.1145	0.5691	0.0674	-0.2024	0.0019	0.1595	-0.0233	0.1852	0.0892	-0.1392	-0.0098	0.2673	-0.0309	-0.0266	0.2598	0.064	0.3072	78.2692	55.0064	57.6369
3	0.5512	0.0806	0.3052	0.7029	-0.3205	0.3851	0.3103	-0.0591	-0.4197	0.1326	0.1389	0.1585	0.2253	-0.0552	0.818	0.4344	-0.1579	-0.21	0.2647	0.0906	0.5583	59.5274	38.5227	21.6997
4	0.1941	0.0154	0.1917	0.0018	0.0147	0.1752	0.0328	-0.0442	-0.0138	-0.0651	0.147	0.2686	-0.0318	-0.0496	0.2857	0.4111	-0.2781	0.0163	-0.2002	0.1732	0.2582	81.4885	57.1453	50.8271
5	0.5074	0.0503	0.036	0.5096	-0.0157	0.5219	0.0411	0.1299	-0.1532	-0.1451	0.0013	0.0905	0.1571	-0.0861	0.0026	0.3003	-0.0266	-0.0912	0.204	-0.0106	0.3096	82.5834	45.2684	18.7058
6	0.2632	-0.1037	-0.1103	1.3612	-0.0872	0.0623	-0.0101	-0.3514	0.4951	-0.1621	-0.0677	0.4515	-0.202	-0.1457	-0.0981	0.2604	0.0713	-0.1077	0.7066	-0.0753	0.6538	55.5251	70.551	14.7913
7	0.0743	0.056	0.014	0.0232	-0.0136	0.0491	-0.0231	0.0687	0.1176	0.0416	-0.2353	0.2153	-0.3972	-0.1985	-0.0007	0.2841	0.0455	-0.0005	0.4121	0.0338	0.4736	58.0178	67.2596	46.142
8	0.1017	0.0234	-0.1411	0.0324	-0.0127	0.2058	-0.0263	-0.226	-0.091	-0.0718	0.1327	0.0126	-0.0554	-0.1585	0.7509	0.2212	0.1401	-0.2824	0.1513	0.0664	0.2024	84.9643	50.1153	18.9759
9	0.7265	0.043	0.0788	1.0881	-0.0228	0.7951	-0.0121	0.0621	0.0839	-0.2245	-0.0422	0.2294	0.0144	-0.2158	-0.2637	0.0698	0.0172	0.0206	0.192	-0.0278	0.1939	82.9975	117.5523	27.6323
10	0.6587	0.2312	0.005	1.5184	0.0672	0.4243	-0.0249	-0.0015	-0.0008	-0.1597	0.0664	0.3755	0.1412	-0.1878	0.1124	0.106	0.0111	0.0459	0.2515	-0.0554	0.2504	74.3988	118.5014	36.6497
11	0.8261	0.3048	0.4361	0.6516	0.7783	0.9638	-0.2391	-0.4994	-0.0097	0.4264	-0.0981	-0.0928	0.3137	-0.0732	-0.3962	0.3611	0.0868	0.0292	0.2858	0.1319	0.3364	109.6892	96.0756	50.1635
12	0.0026	0.0275	-0.0244	0.4789	-0.3624	0.3042	0.2488	-0.0815	-0.0101	-0.3097	0.182	0.0047	-0.0997	-0.6318	0.0371	0.1407	-0.021	0.0416	0.2259	0.0619	0.3549	81.1587	121.1053	34.0863
13	0.7685	-0.0013	0.1219	0.8593	-0.0742	0.4121	-0.0028	-0.0652	0.1769	0.1646	-0.0474	0.1411	-0.1917	-0.0993	-0.2222	0.2754	0.0345	0.0357	0.1894	-0.0693	0.3276	84.3083	152.9448	47.0078
14	0.3657	-0.1693	-0.0045	1.1336	0.0875	0.0793	-0.0247	-0.0752	0.0902	0.1764	-0.0616	0.3313	-0.2666	-0.0882	-0.3268	0.2412	0.064	-0.0023	0.2706	-0.0698	0.4153	74.229	150.9924	40.0649
15	1.0605	-0.0748	0.1379	0.1165	0.4068	1.4856	-0.2308	0.3061	0.2021	-0.0329	0.0347	0.0982	-0.71	-0.181	-0.1459	0.4918	-0.0221	0.03	0.2927	0.0902	0.9271	103.432	175.3569	20.4027
16	0.052	0.0042	0.0164	0.0229	-0.011	0.0106	0.128	0.0168	-0.09	0.1878	0.0578	0.0636	0.1548	-0.3007	0.0001	0.2474	0.0373	0.081	0.2221	-0.0214	0.3344	81.5554	149.3715	40.9085

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 30:391)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 392:519)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 520:536)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 537:537)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 30:504)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 505:522)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 523:536)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 537:537)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 28:391)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 392:520)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 521:536)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 537:537)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 30:390)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 391:516)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 517:536)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 537:537)

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