PDB-6oo1: Dehaloperoxidase B in complex with substrate o-cresol

ID or keywords:

Entry

Database: PDB / ID: 6oo1

Title

Dehaloperoxidase B in complex with substrate o-cresol

Components

Dehaloperoxidase B

Keywords

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

Function / homology

Function and homology information

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

Biological species

Amphitrite ornata (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.602 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	Jul 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6oo1.cif.gz	140.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6oo1.ent.gz	108.5 KB	Display	PDB format
PDBx/mmJSON format	6oo1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6oo1_validation.pdf.gz	516.3 KB	Display	wwPDB validaton report
Full document	6oo1_full_validation.pdf.gz	521 KB	Display
Data in XML	6oo1_validation.xml.gz	2.6 KB	Display
Data in CIF	6oo1_validation.cif.gz	7.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oo/6oo1 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/6oo1	HTTPS FTP

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Related structure data

Related structure data	6ongC 6onkC 6onrC 6onxC 6onzC 6oo6C 6oo8C 3ixfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5vts-1 6ch5-1 3ppt-d 6e6m-3 6ay1-8 4hr2-1 1wsb-d 1j8q-d 6vdt-1 6vdw-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

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

1

A: Dehaloperoxidase B

hetero molecules

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

2

B: Dehaloperoxidase B

hetero molecules

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

Unit cell

Length a, b, c (Å)	59.273, 67.690, 67.680
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
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) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 232 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-JZ0 / o-cresol / ortho-cresol,2-methylphenol Mass: 108.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₈O
#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.: 215 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.14 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2000, 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: 1.6→37.26 Å / Num. obs: 34115 / % possible obs: 98.44 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / B_iso Wilson estimate: 16.6 Å² / CC_1/2: 0.997 / R_pim(I) all: 0.025 / R_rim(I) all: 0.054 / Χ²: 1.076 / Net I/σ(I): 28.6
Reflection shell	Resolution: 1.6→1.643 Å / Redundancy: 2 % / Num. unique obs: 2202 / CC_1/2: 0.721 / R_pim(I) all: 0.36 / R_rim(I) all: 0.594 / Χ²: 1.077 / % possible all: 85.97

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ixf

3ixf

Resolution: 1.602→37.26 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.952 / SU B: 3.624 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.096
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1986	1840	5.118 %
R_work	0.171	-	-
all	0.172	-	-
obs	-	35955	98.445 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 18.364 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.346 Å²	0 Å²	-0 Å²
2-	-	-0.692 Å²	0 Å²
3-	-	-	-0.654 Å²

Refinement step

Cycle: LAST / Resolution: 1.602→37.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2142	0	156	215	2513

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	2861
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	2530
X-RAY DIFFRACTION	r_angle_refined_deg	1.53	1.707	3925
X-RAY DIFFRACTION	r_angle_other_deg	1.502	1.62	5929
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.45	5	384
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.215	23.553	152
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.331	15	496
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.477	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	340
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3454
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	659
X-RAY DIFFRACTION	r_nbd_refined	0.258	0.2	752
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	2279
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	1333
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	990
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	186
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.019	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.173	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.119	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	0.455	0.885	1342
X-RAY DIFFRACTION	r_mcbond_other	0.453	0.884	1341
X-RAY DIFFRACTION	r_mcangle_it	0.792	1.328	1740
X-RAY DIFFRACTION	r_mcangle_other	0.792	1.329	1741
X-RAY DIFFRACTION	r_scbond_it	0.782	1.072	1519
X-RAY DIFFRACTION	r_scbond_other	0.762	1.067	1512
X-RAY DIFFRACTION	r_scangle_it	1.144	1.566	2164
X-RAY DIFFRACTION	r_scangle_other	1.126	1.557	2153
X-RAY DIFFRACTION	r_lrange_it	5.204	11.904	3581
X-RAY DIFFRACTION	r_lrange_other	5.17	11.628	3547

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 (%)
1.602-1.643	0.256	108	0.248	2202	X-RAY DIFFRACTION	85.9695
1.643-1.688	0.246	134	0.229	2313	X-RAY DIFFRACTION	95.6607
1.688-1.737	0.224	127	0.212	2391	X-RAY DIFFRACTION	99.1729
1.737-1.79	0.222	114	0.196	2335	X-RAY DIFFRACTION	99.9592
1.79-1.849	0.229	127	0.182	2258	X-RAY DIFFRACTION	100
1.849-1.914	0.218	84	0.169	2231	X-RAY DIFFRACTION	99.9568
1.914-1.986	0.18	110	0.158	2078	X-RAY DIFFRACTION	100
1.986-2.067	0.212	102	0.155	2049	X-RAY DIFFRACTION	100
2.067-2.159	0.155	131	0.145	1938	X-RAY DIFFRACTION	100
2.159-2.264	0.198	108	0.143	1886	X-RAY DIFFRACTION	99.9499
2.264-2.386	0.161	95	0.149	1765	X-RAY DIFFRACTION	100
2.386-2.53	0.165	96	0.143	1690	X-RAY DIFFRACTION	100
2.53-2.704	0.182	104	0.161	1587	X-RAY DIFFRACTION	99.9409
2.704-2.92	0.206	57	0.17	1518	X-RAY DIFFRACTION	100
2.92-3.198	0.258	75	0.175	1373	X-RAY DIFFRACTION	99.7932
3.198-3.573	0.195	83	0.174	1238	X-RAY DIFFRACTION	99.6981
3.573-4.122	0.173	62	0.154	1115	X-RAY DIFFRACTION	99.4088
4.122-5.039	0.179	46	0.165	965	X-RAY DIFFRACTION	98.9237
5.039-7.087	0.258	53	0.225	735	X-RAY DIFFRACTION	98.7469
7.087-37.26	0.179	24	0.212	448	X-RAY DIFFRACTION	95.935

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	0.7669	-0.2294	0.1185	0.6144	-0.6578	0.729	-0.0369	0.0006	-0.0844	0.048	0.0471	0.0301	-0.0447	-0.0566	-0.0102	0.1099	-0.0008	-0.0018	0.0964	-0.0009	0.0972	-0.1141	-1.6544	-23.8842
2	2.1539	0.5314	1.4517	1.8351	1.0925	4.5904	-0.1341	0.0091	0.1747	0.0443	-0.057	-0.1314	0.1964	0.1878	0.1911	0.0778	0.0071	-0.0228	0.0893	0.0292	0.1269	16.4168	-4.3351	-15.2215
3	4.4801	0.5073	-0.1706	10.1164	-5.5553	3.0559	-0.0706	-0.122	0.2744	0.3464	-0.0167	-0.1235	-0.1827	-0.0021	0.0873	0.1641	-0.0286	-0.0286	0.0669	-0.0472	0.0876	11.3373	-1.025	-7.8268
4	1.5906	-1.1495	0.5792	3.1451	-0.4433	0.212	-0.182	-0.1001	0.0147	0.2733	0.1702	0.0604	-0.0619	-0.0396	0.0118	0.1642	0.0311	0.0328	0.0871	-0.0007	0.0578	2.586	-5.2609	-10.7326
5	1.2321	0.2633	-0.9044	0.8684	-0.8933	1.2707	0.0717	-0.0057	0.068	0.0688	0.0159	0.0392	-0.0889	-0.0098	-0.0876	0.1145	-0.0098	0.0071	0.0889	-0.0151	0.1046	2.3137	12.6441	-25.1167
6	0.2846	-0.5994	-0.7083	1.3913	0.9767	3.8243	-0.0731	-0.0045	0.0296	0.3358	0.0004	-0.1013	-0.5532	0.039	0.0727	0.3744	-0.1039	-0.0522	0.1005	-0.0158	0.0289	8.9811	13.2098	-12.2173
7	3.2859	0.8109	2.4425	7.4488	3.4232	2.9401	-0.1985	0.0891	0.0656	0.1278	0.1634	-0.1488	-0.0922	0.1751	0.0351	0.0576	-0.0252	-0.0561	0.1266	0.0759	0.145	15.6186	5.854	-18.919
8	2.9541	0.7873	1.8039	3.3965	2.2249	2.068	0.0602	0.2195	-0.0017	0.1171	-0.1039	0.0061	0.0845	0.0534	0.0437	0.1016	0.0057	0.0044	0.086	0.0167	0.138	8.1582	-3.3374	-27.7733
9	3.0824	3.2146	1.497	4.8045	1.8626	1.8679	0.0721	0.1049	-0.0759	0.0226	-0.0806	-0.2066	0.0404	0.0467	0.0086	0.0733	0.0024	0.0125	0.0856	-0.0021	0.1126	6.8462	3.2117	-32.1771
10	0.8414	-0.8748	2.022	6.4098	-0.5933	5.3212	-0.0482	-0.0281	0.0772	0.1971	-0.0623	-0.5471	-0.1744	-0.0639	0.1106	0.1653	-0.0742	-0.0618	0.0505	-0.0112	0.1776	14.8497	15.0249	-21.639
11	0.7179	0.4647	-0.2386	0.5649	-0.4224	0.3594	0.0102	-0.0763	0.0011	-0.0434	-0.0288	-0.0362	0.0302	-0.0112	0.0187	0.1186	-0.0156	0.01	0.1	0.0145	0.0965	-17.3405	6.8923	-15.0608
12	3.3503	-1.9938	1.4556	3.894	-0.5888	1.2793	-0.0958	0.2949	-0.155	0.1627	0.07	0.1424	0.0979	-0.0109	0.0257	0.1071	-0.0369	0.008	0.1149	-0.0284	0.069	-28.0611	-7.2131	-13.5443
13	9.8716	1.8233	-6.5887	2.1231	-0.4556	4.727	-0.0646	-0.5166	-0.5034	-0.0529	-0.3186	-0.0132	0.0437	0.272	0.3833	0.0989	0.0621	0.0215	0.1805	0.0855	0.0687	-18.1421	-6.7331	-6.0949
14	2.1202	-0.7603	-0.1449	4.2035	-3.1505	5.2475	-0.0094	0.0424	-0.0996	-0.0401	0.061	0.0979	0.203	-0.0187	-0.0516	0.0957	0.004	0.0201	0.0901	0.0245	0.1018	-15.3889	-3.5721	-17.6802
15	1.6097	-1.4809	1.4301	2.2219	-1.6468	1.4036	0.0408	0.0617	-0.0297	-0.1057	-0.053	-0.0182	0.055	0.0633	0.0122	0.1162	0.011	0.0139	0.0923	0.0214	0.0979	-17.3718	10.2285	-29.1551
16	0.3003	1.1359	0.4915	6.2129	1.1748	1.0569	0.1807	-0.0168	-0.1504	-0.1601	0.1638	-0.242	0.5458	-0.1229	-0.3444	0.4317	-0.0765	-0.2317	0.0732	0.0379	0.1548	-23.0964	1.4072	-32.5121
17	8.0235	-6.0832	-4.2788	9.4114	3.5232	3.3629	-0.0911	0.0787	-0.4288	0.0748	-0.1922	0.2445	0.1494	-0.1021	0.2833	0.1074	-0.062	-0.0488	0.0846	0.0178	0.0897	-28.5433	-3.2648	-26.2592
18	3.8807	3.8057	2.214	3.7459	2.2246	3.1984	0.0033	-0.0002	0.2224	-0.0006	0.0364	0.2039	0.1195	-0.138	-0.0398	0.1005	-0.011	0.0045	0.1385	0.0085	0.0829	-25.2845	9.9563	-15.503
19	3.3613	1.8869	2.8328	1.1379	1.2299	4.2502	0.0433	-0.0143	0.1704	0.0245	0.0098	0.1093	0.0249	-0.1311	-0.0531	0.0963	0.0053	0.0082	0.0953	0.0159	0.0964	-22.183	15.8944	-20.4292
20	0.0062	0.0145	0.1047	0.1821	1.2589	8.7524	0.0528	-0.0083	-0.0145	0.0537	-0.0327	-0.0031	0.4087	-0.408	-0.02	0.2407	-0.0578	-0.0961	0.1317	0.0162	0.0405	-30.4411	5.6055	-31.4966

Refinement TLS group

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

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 232 molecules

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-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 232 molecules

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Movie

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Structure viewers

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Open data

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 232 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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Yorodumi