PDB-6oo8: Dehaloperoxidase B in complex with substrate pentachlorophenol

ID or keywords:

Entry

Database: PDB / ID: 6oo8

Title

Dehaloperoxidase B in complex with substrate pentachlorophenol

Components

Dehaloperoxidase B

Keywords

OXIDOREDUCTASE / heme peroxidase / peroxygenase / heme cofactor / oxygen binding

Function / homology

Function and homology information

oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function

Biological species

Amphitrite ornata (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Ghiladi, R.A. / de Serrano, V.S. / Malewschik, T.

Citation

Journal: Arch.Biochem.Biophys. / Year: 2019
Title: The multifunctional globin dehaloperoxidase strikes again: Simultaneous peroxidase and peroxygenase mechanisms in the oxidation of EPA pollutants.
Authors: Malewschik, T. / de Serrano, V. / McGuire, A.H. / Ghiladi, R.A.

History

Deposition	Apr 22, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6oo8.cif.gz	149.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6oo8.ent.gz	120.3 KB	Display	PDB format
PDBx/mmJSON format	6oo8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6oo8_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	6oo8_full_validation.pdf.gz	1.8 MB	Display
Data in XML	6oo8_validation.xml.gz	20.1 KB	Display
Data in CIF	6oo8_validation.cif.gz	26.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oo/6oo8 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/6oo8	HTTPS FTP

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Related structure data

Related structure data	6ongC 6onkC 6onrC 6onxC 6onzC 6oo1C 6oo6C C: citing same article (ref.)
Similar structure data	6oo6-1 6vdv-1 6vd6-1 6onr-1 4kmv-2 6onx-1 6vdt-1 6vdu-2 6vdy-1 6vd4-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#206 - Feb 2017 Globin Evolution similarity (1) #41 - May 2003 Hemoglobin similarity (1) #159 - Mar 2013 Erythrocruorin similarity (2) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#206 - Feb 2017
Globin Evolution
similarity (1)
#41 - May 2003
Hemoglobin
similarity (1)
#159 - Mar 2013
Erythrocruorin
similarity (2)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#142 - Oct 2011
PDB Pioneers
similarity (1)

Deposited unit

A: Dehaloperoxidase B

B: Dehaloperoxidase B

hetero molecules

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

1

A: Dehaloperoxidase B

hetero molecules

defined by author&software
Evidence: gel filtration
16.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Dehaloperoxidase B

hetero molecules

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

Unit cell

Length a, b, c (Å)	60.690, 67.220, 67.580
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Dehaloperoxidase B Mass: 15414.462 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amphitrite ornata (invertebrata) / Plasmid: pET16b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Gold(DE3)pLysS AG / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 155 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PCI / PENTACHLOROPHENOL Mass: 266.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆HCl₅O
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 44.98 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 5000, ammonium sulphate, sodium cacodylate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 21, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→37.51 Å / Num. obs: 23034 / % possible obs: 92.36 % / Observed criterion σ(I): 1.5 / Redundancy: 4.6 % / B_iso Wilson estimate: 20.1 Å² / CC_1/2: 0.997 / R_pim(I) all: 0.042 / R_rim(I) all: 0.095 / Χ²: 0.91 / Net I/σ(I): 10.6
Reflection shell	Resolution: 1.8→1.847 Å / Redundancy: 4.4 % / Num. unique obs: 1742 / CC_1/2: 0.872 / R_pim(I) all: 0.371 / R_rim(I) all: 0.835 / Χ²: 0.93 / % possible all: 96.12

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→37.51 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.943 / SU B: 5.932 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21773	1229	5.1 %	RANDOM
R_work	0.17632	-	-	-
obs	0.17845	23034	92.36 %	-

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: 22.372 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.03 Å²	0 Å²	-0 Å²
2-	-	-1.6 Å²	0 Å²
3-	-	-	-1.43 Å²

Refinement step

Cycle: 1 / Resolution: 1.8→37.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2149	0	152	141	2442

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	2887
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.018	2520
X-RAY DIFFRACTION	r_angle_refined_deg	1.691	1.71	3970
X-RAY DIFFRACTION	r_angle_other_deg	1.498	1.625	5908
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.528	5	377
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.615	22.688	160
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.875	15	508
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.536	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	341
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3486
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	662
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	0.705	1.333	1334
X-RAY DIFFRACTION	r_mcbond_other	0.702	1.333	1333
X-RAY DIFFRACTION	r_mcangle_it	1.138	1.998	1722
X-RAY DIFFRACTION	r_mcangle_other	1.138	1.999	1723
X-RAY DIFFRACTION	r_scbond_it	1.02	1.645	1553
X-RAY DIFFRACTION	r_scbond_other	1.005	1.639	1546
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.503	2.43	2214
X-RAY DIFFRACTION	r_long_range_B_refined	9.404	18.768	3771
X-RAY DIFFRACTION	r_long_range_B_other	9.408	18.677	3753
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.267	91	-
R_work	0.235	1742	-
obs	-	-	96.12 %

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	1.0259	-0.6866	0.9702	0.8653	-0.589	1.4445	-0.0491	-0.0569	-0.1131	-0.0284	0.0112	0.0312	0.0133	-0.0917	0.0379	0.0674	-0.0009	0.0082	0.0925	0.0183	0.0776	-0.2881	-1.6008	-23.898
2	1.0225	-2.6282	1.0829	8.4107	0.1602	6.395	-0.1919	0.1196	0.2054	0.5493	-0.1417	-0.4686	-0.1252	0.3971	0.3336	0.0919	-0.0123	-0.031	0.0694	0.0504	0.099	16.182	-4.5385	-15.628
3	4.6877	-1.6557	-0.9301	2.8983	-0.0509	0.2476	0.094	-0.3592	0.1571	-0.0005	-0.0653	-0.0262	-0.0277	0.1063	-0.0287	0.1185	-0.0115	-0.0572	0.0751	0.0076	0.0771	12.2118	-0.8912	-7.4934
4	1.096	-1.4143	1.0233	4.6253	-1.0106	1.0097	-0.1056	-0.0661	0.0107	0.209	0.0598	0.0856	-0.0774	-0.0259	0.0458	0.0608	0.0059	0.042	0.1021	0.0194	0.0653	2.691	-5.0501	-10.7401
5	1.6751	1.324	-0.4451	1.7013	-1.2159	2.3829	0.0092	-0.0121	0.0895	0.1644	-0.0918	0.024	-0.198	-0.0485	0.0826	0.077	0.0091	-0.0271	0.0733	-0.0078	0.0797	2.3287	12.699	-25.2996
6	12.5823	-10.4503	0.4517	11.1555	3.3925	5.779	-0.2467	-0.1943	-0.105	0.1288	0.3257	0.0018	-0.2636	0.2414	-0.0791	0.367	-0.143	-0.0872	0.0668	0.0338	0.028	8.9969	13.2304	-12.4082
7	5.8678	3.4078	-0.0389	6.7805	4.6759	4.5997	-0.0352	0.0732	0.2697	0.1117	0.4427	-0.2663	0.1102	0.404	-0.4076	0.169	-0.0517	-0.1319	0.0755	0.031	0.1558	15.5356	5.9299	-19.2904
8	3.7144	1.6916	2.6669	5.516	0.6711	2.0177	0.115	0.3185	0.0518	0.1403	-0.2498	-0.018	0.1086	0.3039	0.1347	0.0583	0.034	0.0888	0.0829	0.0646	0.1632	8.0457	-3.3686	-28.1838
9	3.4281	3.4751	1.7003	5.6897	0.7284	1.4943	0.0349	0.1493	-0.058	-0.1269	-0.1658	-0.249	0.0749	0.1336	0.1309	0.0471	0.0297	0.0268	0.0955	0.002	0.0843	6.6055	3.1074	-32.371
10	0.9261	0.0482	0.9595	0.0289	0.1759	10.2653	0.2062	0.4721	0.1766	0.0714	-0.0244	-0.0605	-0.05	0.2769	-0.1818	0.2359	0.0022	-0.122	0.3241	0.2123	0.2188	14.6072	15.03	-22.1254
11	0.4688	0.4717	-0.353	2.1968	-0.621	0.4969	-0.0894	0.0025	-0.005	0.1901	0.1121	-0.2426	-0.0323	-0.0978	-0.0226	0.0912	0.0174	-0.0216	0.0895	-0.0043	0.0658	-17.4273	6.818	-14.8712
12	0.0572	0.0861	0.109	0.1384	0.1479	0.2405	-0.0269	0.0128	-0.0197	-0.0627	0.0823	-0.0177	-0.0355	-0.0875	-0.0555	0.186	-0.1501	-0.0213	0.4309	0.0793	0.0311	-28.153	-7.2538	-13.3837
13	4.1313	1.9581	-4.4402	1.0774	-2.714	7.2607	-0.0706	-0.4688	-0.2913	-0.0931	-0.192	-0.1272	0.3178	0.3547	0.2626	0.0677	0.0225	-0.0045	0.1072	0.0544	0.0419	-18.2641	-6.6394	-5.9299
14	1.1743	-0.5847	1.2898	3.9048	-2.1598	4.352	0.0275	-0.0776	-0.0353	-0.1003	0.0196	0.0927	0.2361	0.0387	-0.047	0.0793	0.0118	-0.0038	0.0857	0.0287	0.0622	-15.5872	-3.5561	-17.4179
15	1.2494	-0.4443	1.2182	2.4532	-0.8908	1.3262	0.0532	0.045	0.0862	-0.1087	-0.0933	-0.0761	0.0891	0.0463	0.0401	0.0557	0.0029	0.0108	0.0942	0.008	0.0789	-17.6654	10.1749	-28.9361
16	1.3526	2.2786	-0.9147	4.1757	-0.7721	2.4874	0.1773	0.0201	-0.1136	0.2597	0.0836	-0.3395	0.1611	-0.0259	-0.2609	0.2507	-0.0234	-0.0912	0.054	0.0134	0.0939	-23.4071	1.3206	-32.3286
17	8.1422	-7.365	-4.031	11.3602	-0.0663	4.9494	-0.3253	0.0512	-0.4891	0.3329	-0.0199	0.338	0.1801	-0.0466	0.3452	0.117	-0.0536	0.0118	0.0685	0.014	0.0619	-28.8369	-3.3215	-26.1316
18	3.5805	3.4504	2.379	3.4464	1.7287	4.2865	0.046	0.0048	0.2729	-0.0017	0.0523	0.3153	0.281	-0.1322	-0.0984	0.1077	0.0133	-0.0164	0.1024	-0.0171	0.0646	-25.4539	9.8996	-15.3308
19	4.1109	1.7255	3.3647	0.7898	1.1214	4.5481	0.0621	-0.1032	0.2229	0.0727	-0.0108	0.1323	0.0326	-0.2261	-0.0514	0.0992	0.0214	0.0083	0.0906	-0.0105	0.0727	-22.3349	15.8432	-20.2246
20	0.5031	-0.1618	1.7862	0.2628	-0.5525	6.3443	0.0884	-0.1732	-0.0114	-0.0922	-0.0471	-0.0948	0.277	-0.6266	-0.0413	0.1299	-0.0447	-0.0348	0.1681	0.0907	0.0888	-30.8005	5.5014	-31.2936

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 26
2	X-RAY DIFFRACTION	2	A	27 - 33
3	X-RAY DIFFRACTION	3	A	34 - 37
4	X-RAY DIFFRACTION	4	A	38 - 60
5	X-RAY DIFFRACTION	5	A	61 - 83
6	X-RAY DIFFRACTION	6	A	84 - 90
7	X-RAY DIFFRACTION	7	A	91 - 99
8	X-RAY DIFFRACTION	8	A	100 - 111
9	X-RAY DIFFRACTION	9	A	112 - 128
10	X-RAY DIFFRACTION	10	A	129 - 137
11	X-RAY DIFFRACTION	11	B	1 - 30
12	X-RAY DIFFRACTION	12	B	31 - 39
13	X-RAY DIFFRACTION	13	B	40 - 50
14	X-RAY DIFFRACTION	14	B	51 - 60
15	X-RAY DIFFRACTION	15	B	61 - 77
16	X-RAY DIFFRACTION	16	B	78 - 86
17	X-RAY DIFFRACTION	17	B	87 - 94
18	X-RAY DIFFRACTION	18	B	95 - 111
19	X-RAY DIFFRACTION	19	B	112 - 128
20	X-RAY DIFFRACTION	20	B	129 - 137

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