PDB-6oo6: Dehaloperoxidase B in complex with substrate p-cresol

ID or keywords:

Entry

Database: PDB / ID: 6oo6

Title

Dehaloperoxidase B in complex with substrate p-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: 2.1 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	Sep 25, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6oo6.cif.gz	142.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6oo6.ent.gz	114.8 KB	Display	PDB format
PDBx/mmJSON format	6oo6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6oo6_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6oo6_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6oo6_validation.xml.gz	15.5 KB	Display
Data in CIF	6oo6_validation.cif.gz	21.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oo/6oo6 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/6oo6	HTTPS FTP

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Related structure data

Related structure data	6ongC 6onkC 6onrC 6onxC 6onzC 6oo1C 6oo8C C: citing same article (ref.)
Similar structure data	6vd6-1 6ong-1 6oo8-1 6vdy-1 6vd4-1 6vdw-2 6ch5-1 6vdr-2 6vds-1 6vdt-1 4kjt-2 7lhn-2 4hsx-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

32.5 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
16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Dehaloperoxidase B

hetero molecules

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

Unit cell

Length a, b, c (Å)	60.505, 67.540, 67.625
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, 156 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-PCR / P-CRESOL Mass: 108.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₈O
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.24 Å³/Da / Density % sol: 45.11 %
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 twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.829
1	1	-H, -L, -K	2	0.171

Reflection

Resolution: 2.1→45.09 Å / Num. obs: 15319 / % possible obs: 95.51 % / Observed criterion σ(I): 1.5 / Redundancy: 8.4 % / B_iso Wilson estimate: 14.1 Å² / CC_1/2: 0.996 / R_pim(I) all: 0.035 / R_rim(I) all: 0.1 / Χ²: 0.92 / Net I/σ(I): 16.6

Reflection shell

Resolution: 2.1→2.152 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 11.9 / Num. unique obs: 1100 / CC_1/2: 0.992 / R_pim(I) all: 0.055 / R_rim(I) all: 0.164 / Χ²: 0.65 / % possible all: 96.51

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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: 2.1→45.09 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.885 / SU B: 8.14 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22432	711	4.4 %	RANDOM
R_work	0.16046	-	-	-
obs	0.16311	15319	95.51 %	-

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: 15.421 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	25.89 Å²	0 Å²	0 Å²
2-	-	-15.52 Å²	-0 Å²
3-	-	-	-10.37 Å²

Refinement step

Cycle: 1 / Resolution: 2.1→45.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2138	0	116	149	2403

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	2792
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	2478
X-RAY DIFFRACTION	r_angle_refined_deg	1.521	1.701	3857
X-RAY DIFFRACTION	r_angle_other_deg	1.396	1.618	5799
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.701	5	383
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.949	22.715	151
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.246	15	501
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.734	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	340
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3415
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	658
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	0.323	0.918	1336
X-RAY DIFFRACTION	r_mcbond_other	0.321	0.918	1335
X-RAY DIFFRACTION	r_mcangle_it	0.564	1.379	1733
X-RAY DIFFRACTION	r_mcangle_other	0.564	1.38	1734
X-RAY DIFFRACTION	r_scbond_it	0.469	1.018	1456
X-RAY DIFFRACTION	r_scbond_other	0.445	1.01	1449
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.721	1.506	2089
X-RAY DIFFRACTION	r_long_range_B_refined	2.906	11.473	3473
X-RAY DIFFRACTION	r_long_range_B_other	2.87	11.36	3454
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.098→2.152 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.217	60	-
R_work	0.15	1100	-
obs	-	-	96.51 %

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	0.8021	-0.4473	0.596	0.6402	-0.3548	1.4646	-0.0197	-0.1123	-0.0019	-0.088	0.0569	-0.0106	0.026	-0.1059	-0.0372	0.0697	-0.0072	0.0071	0.0523	0.0103	0.0406	-0.0866	-1.5255	-24.03
2	1.3754	0.0939	-1.7157	2.7499	1.9499	4.2205	-0.1544	0.0341	-0.0852	-0.0223	0.1454	-0.2928	-0.043	0.1633	0.009	0.1457	0.0002	-0.0157	0.0873	0.0395	0.0832	16.5576	-4.3396	-15.4857
3	5.592	4.4924	-2.7841	4.752	-2.8186	1.6824	0.1602	-0.2045	0.1113	0.0206	-0.2044	-0.1007	-0.0255	0.1233	0.0442	0.0958	0.0116	-0.0255	0.015	-0.0048	0.0602	11.4726	-0.957	-8.042
4	1.7663	-0.8553	0.289	2.2524	-1.0471	0.5282	-0.0908	-0.1472	0.0088	0.091	0.1321	0.0427	-0.005	-0.0514	-0.0412	0.0754	-0.0049	0.0059	0.0704	-0.005	0.0286	2.5542	-5.0244	-10.918
5	1.4236	0.7894	-0.0878	1.1146	-1.4414	3.3446	-0.0124	0.0555	0.0378	0.0723	-0.0388	0.0677	-0.1912	-0.0403	0.0512	0.0323	0.0003	-0.0086	0.0854	-0.0478	0.0667	2.5101	12.8021	-25.339
6	0.5293	-1.2001	-0.036	4.4489	-0.5369	0.2239	0.086	-0.1113	-0.1002	0.1258	-0.1571	0.0586	-0.1171	0.1556	0.0711	0.0716	-0.0875	-0.0511	0.1289	0.0534	0.0452	9.1443	13.2675	-12.4321
7	3.2589	1.5675	0.2622	2.8493	2.5901	2.9686	-0.054	0.1189	0.1356	0.0366	0.1069	-0.0486	0.0377	0.1141	-0.0529	0.0269	-0.0221	-0.0579	0.0547	0.0549	0.1273	15.6543	5.8448	-19.2424
8	3.3052	1.4788	1.4437	2.9292	0.0294	0.8001	0.0533	0.1378	0.0026	-0.1029	-0.1152	-0.1985	0.0714	0.1093	0.0619	0.1095	0.0289	0.0547	0.0379	0.0096	0.0475	8.1352	-3.3368	-28.3508
9	3.1477	2.2751	1.5313	3.1009	-0.0274	1.6285	0.0719	0.1322	0.0369	-0.107	-0.1189	-0.0146	0.1612	0.2294	0.0469	0.0387	0.0191	0.0242	0.0495	0.0009	0.0523	6.7355	3.2237	-32.3673
10	0.2784	-1.0698	0.6889	4.1132	-2.6494	1.7067	-0.009	0.0939	0.1434	0.0471	-0.3561	-0.5609	-0.0309	0.2297	0.3651	0.0493	-0.0231	-0.0382	0.052	0.044	0.1193	14.7848	15.0395	-22.1352
11	1.2411	1.0086	-0.8039	2.1274	-0.3191	0.6248	0.0003	0.0651	-0.0145	0.2398	0.0507	-0.2354	0.0228	-0.044	-0.051	0.1174	0.0004	-0.0368	0.0277	-0.0048	0.0394	-17.542	6.816	-14.9577
12	2.0209	-2.1582	1.9633	2.3486	-2.075	1.9184	-0.3991	-0.4048	-0.0924	0.4035	0.5252	0.0284	-0.395	-0.3512	-0.1261	0.2717	-0.0545	-0.0286	0.31	-0.0873	0.1589	-28.2966	-7.3818	-13.5654
13	5.1108	1.0079	-3.6149	0.199	-0.7048	5.0327	-0.0888	-0.1987	-0.3559	-0.0173	-0.0452	-0.0682	0.0027	0.2405	0.1339	0.0694	-0.0112	-0.0226	0.0355	0.0177	0.0734	-18.4353	-6.9548	-6.1589
14	0.6358	-1.4306	1.1289	7.085	-3.2875	2.154	0.014	0.0501	-0.0245	-0.0221	0.0063	0.0432	0.0138	0.0637	-0.0203	0.0407	0.0075	-0.0221	0.0393	-0.0148	0.0815	-15.305	-3.541	-17.6952
15	0.7528	-0.389	1.0343	3.2425	-1.216	1.5817	0.0515	0.0244	0.0066	-0.037	-0.0508	-0.0561	0.0611	0.0382	-0.0007	0.0427	0.0081	0.0181	0.0604	0.0088	0.0693	-17.4661	10.2214	-29.0218
16	2.5036	-1.8564	1.8416	1.3774	-1.3643	1.3561	0.0021	-0.0666	0.0228	-0.0105	0.0201	-0.0269	0.0318	-0.053	-0.0222	0.1021	-0.037	-0.101	0.0257	0.03	0.1261	-23.1579	1.4204	-32.5919
17	2.8319	-2.6931	-1.2793	7.2847	-1.4075	3.4119	-0.0559	-0.0941	-0.2501	0.1698	-0.0018	0.0713	0.1372	0.0897	0.0577	0.0423	-0.0193	-0.0246	0.0442	0.0021	0.0639	-28.5731	-3.3084	-26.3867
18	3.1491	2.5588	2.5782	2.1126	2.235	2.9959	0.0493	-0.0397	0.2064	0.0799	-0.0402	0.1455	0.0676	-0.0899	-0.009	0.1091	0.003	0.0156	0.025	0.013	0.0522	-25.43	9.911	-15.5485
19	3.2874	1.6405	2.7539	0.8557	1.2479	2.9513	0.1262	-0.0947	0.1787	0.0945	-0.0551	0.1399	0.0964	-0.1523	-0.0711	0.0803	-0.0264	0.0208	0.0657	-0.0047	0.0938	-22.2761	15.7483	-20.316
20	0.4818	0.7952	-0.7774	1.3148	-1.2745	1.291	-0.0256	0.0991	0.0606	-0.018	0.1488	0.0931	0.1063	-0.2124	-0.1232	0.1433	-0.1016	-0.0508	0.1067	0.03	0.0356	-30.7572	5.4398	-31.4937

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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Components

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 156 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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