PDB-6vd3: Crystal Structure of Dehaloperoxidase B in Complex with cofactor ...

ID or keywords:

Entry

Database: PDB / ID: 6vd3

Title

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Mesoporphyrin IX and Substrate 4-bromophenol

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: 1.67 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Nonnative Heme Incorporation into Multifunctional Globin Increases Peroxygenase Activity an Order and Magnitude Compared to Native Enzyme
Authors: McGuire, A.H. / Petit, A.R. / Kang, J. / Malewschik, T. / de Serrano, V. / Carey, L.M. / Ghiladi, R.A.

History

Deposition	Dec 23, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 23, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jun 30, 2021	Group: Data collection / Category: pdbx_reflns_twin Item: _pdbx_reflns_twin.crystal_id / _pdbx_reflns_twin.diffrn_id
Revision 1.2	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	6vd3.cif.gz	136.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6vd3.ent.gz	105 KB	Display	PDB format
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Validation report

Summary document	6vd3_validation.pdf.gz	480.4 KB	Display	wwPDB validaton report
Full document	6vd3_full_validation.pdf.gz	480.4 KB	Display
Data in XML	6vd3_validation.xml.gz	1.7 KB	Display
Data in CIF	6vd3_validation.cif.gz	5.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vd/6vd3 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/6vd3	HTTPS FTP

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Related structure data

Related structure data	6vd4C 6vd5C 6vd6C 6vdrC 6vdsC 6vdtC 6vduC 6vdvC 6vdwC 6vdxC 6vdyC 3ixfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4kmv-2 6onx-1 6vd6-1 3dr9-2 6vd4-2 6vdu-1 6onk-1 6vdv-1 6onx-2 3ord-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	#220 - Apr 2018 Dehalogenases similarity (1) #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

#220 - Apr 2018
Dehalogenases
similarity (1)
#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

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

1

A: Dehaloperoxidase B

hetero molecules

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

2

B: Dehaloperoxidase B

hetero molecules

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

Unit cell

Length a, b, c (Å)	60.656, 67.432, 67.547
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 (bacteria) / Strain (production host): BL21 / Variant (production host): Gold(DE3)pLysS / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 165 molecules

#2: Chemical	ChemComp-MH0 / Mesoheme Mass: 620.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₆FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-BML / 4-BROMOPHENOL Mass: 173.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₅BrO / Feature type: SUBJECT OF INVESTIGATION
#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.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 157 / 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: 45.1 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M Ammonium Sulfate, MPEG 2000, 29-33%

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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: Jun 16, 2019

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.627
pseudo-merohedral	1	1	-H, -L, -K	2	0.373

Reflection

Resolution: 1.67→33.77 Å / Num. obs: 31197 / % possible obs: 94.53 % / Redundancy: 4.4 % / CC_1/2: 0.997 / Net I/σ(I): 28.6

Reflection shell

Resolution: 1.67→1.71 Å / Num. unique obs: 2039 / CC_1/2: 0.746

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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: 1.67→33.77 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.954 / SU B: 2.579 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.022
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1884	1546	4.956 %
R_work	0.1683	-	-
all	0.169	-	-
obs	-	31197	94.531 %

Solvent computation

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

Displacement parameters

B_iso mean: 17.85 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.225 Å²	0 Å²	0 Å²
2-	-	-2.455 Å²	0 Å²
3-	-	-	-3.77 Å²

Refinement step

Cycle: LAST / Resolution: 1.67→33.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2155	0	120	157	2432

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	2842
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	2549
X-RAY DIFFRACTION	r_angle_refined_deg	1.73	1.648	3912
X-RAY DIFFRACTION	r_angle_other_deg	1.457	1.583	5990
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.478	5	383
X-RAY DIFFRACTION	r_dihedral_angle_other_1_deg	12.796	10	2
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.578	22.675	157
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	15.509	10	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.391	15	529
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.195	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	341
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3432
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	636
X-RAY DIFFRACTION	r_nbd_refined	0.246	0.2	724
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	2269
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	1325
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	999
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.19	0.2	129
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.048	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.229	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.22	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.143	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	0.544	1.175	1340
X-RAY DIFFRACTION	r_mcbond_other	0.542	1.174	1339
X-RAY DIFFRACTION	r_mcangle_it	0.866	1.761	1739
X-RAY DIFFRACTION	r_mcangle_other	0.866	1.762	1740
X-RAY DIFFRACTION	r_scbond_it	0.816	1.332	1502
X-RAY DIFFRACTION	r_scbond_other	0.804	1.327	1495
X-RAY DIFFRACTION	r_scangle_it	1.253	1.977	2151
X-RAY DIFFRACTION	r_scangle_other	1.234	1.969	2140
X-RAY DIFFRACTION	r_lrange_it	3.077	14.446	3463
X-RAY DIFFRACTION	r_lrange_other	3.036	14.363	3449

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 (%)
1.67-1.71	0.29	103	0.3	2039	X-RAY DIFFRACTION	88.6223
1.71-1.757	0.307	126	0.287	2098	X-RAY DIFFRACTION	95.6148
1.757-1.808	0.256	107	0.223	2074	X-RAY DIFFRACTION	95.3234
1.808-1.864	0.222	96	0.192	2031	X-RAY DIFFRACTION	96.594
1.864-1.925	0.208	123	0.196	1958	X-RAY DIFFRACTION	96.2535
1.925-1.992	0.192	114	0.169	1880	X-RAY DIFFRACTION	96.282
1.992-2.067	0.204	101	0.156	1826	X-RAY DIFFRACTION	95.9661
2.067-2.152	0.171	79	0.142	1781	X-RAY DIFFRACTION	95.9752
2.152-2.247	0.213	78	0.149	1711	X-RAY DIFFRACTION	95.0584
2.247-2.356	0.144	99	0.15	1604	X-RAY DIFFRACTION	96.1061
2.356-2.484	0.195	95	0.145	1512	X-RAY DIFFRACTION	94.5851
2.484-2.634	0.172	83	0.139	1451	X-RAY DIFFRACTION	95.0434
2.634-2.815	0.154	73	0.146	1393	X-RAY DIFFRACTION	95.6295
2.815-3.04	0.15	54	0.146	1279	X-RAY DIFFRACTION	94.1384
3.04-3.328	0.18	43	0.165	1193	X-RAY DIFFRACTION	94.4954
3.328-3.719	0.16	40	0.164	1085	X-RAY DIFFRACTION	93.75
3.719-4.29	0.195	38	0.144	952	X-RAY DIFFRACTION	92.093
4.29-5.244	0.216	38	0.165	794	X-RAY DIFFRACTION	91.3282
5.244-7.371	0.142	45	0.206	624	X-RAY DIFFRACTION	90.5277
7.371-33.77	0.196	11	0.231	366	X-RAY DIFFRACTION	85.4875

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	0.5661	-0.3047	0.2504	0.1767	-0.0935	0.5151	-0.0249	-0.0034	-0.0162	0.0053	0.0073	-0.0045	-0.0019	-0.0283	0.0176	0.0856	-0.0023	0.0012	0.0522	0.0116	0.0669	-0.2637	-1.5635	-23.9519
2	1.0716	-1.3854	-0.944	1.8637	1.5817	2.8463	-0.1157	-0.0092	0.1818	0.1367	0.0634	-0.2223	0.0343	0.2385	0.0523	0.1079	0.008	-0.0293	0.0353	-0.0007	0.1327	16.0815	-4.6879	-15.3912
3	8.6631	4.0018	-1.766	2.4867	-1.8892	3.853	0.0227	-0.2063	0.224	0.0324	-0.1616	0.0455	0.0281	0.2282	0.1388	0.0801	0.0004	-0.0348	0.0486	-0.0292	0.0673	11.7934	-0.9556	-6.949
4	3.224	-0.4606	-0.0961	1.4338	0.3333	0.0776	-0.0417	-0.0438	0.0128	0.1194	0.0266	0.0571	0.0289	0.0064	0.0152	0.0832	-0.0021	0.0002	0.0493	0.0036	0.0577	5.2881	-10.5761	-9.5724
5	0.0103	-0.1431	0.1152	2.2448	-2.202	2.7916	-0.0021	0.0028	0.0024	0.0408	-0.0335	-0.0038	-0.0356	0.0271	0.0356	0.0799	-0.0021	0.0012	0.0512	0.004	0.0675	-0.309	3.893	-16.7513
6	1.4358	-0.0069	0.6408	0.0275	0.2321	2.4204	0.0276	-0.0374	0.0017	-0.0039	-0.0186	-0.0098	-0.0543	-0.1383	-0.0091	0.091	-0.0106	-0.0073	0.0404	0.0096	0.0676	4.9229	15.4277	-26.6627
7	2.5395	-1.9062	-0.6726	1.5109	-0.0104	3.4994	-0.0788	-0.076	0.0156	0.0841	0.0575	-0.0156	-0.0975	0.0577	0.0214	0.1143	-0.0466	-0.0183	0.0479	0.0033	0.0393	8.8834	13.6138	-11.77
8	3.5565	1.4639	1.7895	2.1274	1.7767	1.6118	-0.063	-0.043	0.0153	0.0379	0.0799	-0.0367	0.0137	0.0541	-0.0169	0.0946	0.0049	-0.0164	0.0402	0.0256	0.0768	15.4518	5.898	-19.1426
9	1.6141	0.575	0.2091	2.2165	2.1928	2.266	-0.0575	0.0462	-0.0812	0.0351	0.0358	-0.0019	0.0499	0.0535	0.0217	0.0961	0.0103	0.0176	0.0613	0.0141	0.0739	7.9344	-3.3716	-28.2048
10	2.3446	2.0185	1.2679	2.5646	1.2086	1.0253	0.0131	0.0917	-0.034	-0.0197	-0.0473	-0.0897	0.0315	0.0677	0.0342	0.0786	0.0076	0.0107	0.0401	-0.0042	0.0704	6.5842	3.15	-32.4037
11	1.5427	0.5661	1.3211	1.5399	-0.6873	2.9797	0.0414	0.0536	-0.0673	-0.0036	0.0158	-0.1779	0.0071	0.0794	-0.0572	0.0906	-0.0147	-0.0165	0.011	0.01	0.102	14.6166	15.015	-22.1041
12	0.3461	0.2104	-0.1194	0.5556	-0.2785	0.1488	-0.0415	-0.0276	-0.0298	0.0098	0.0141	-0.0628	-0.0116	-0.0243	0.0274	0.0895	0.0022	-0.0002	0.0542	0.0062	0.0677	-14.9932	7.4777	-15.7243
13	2.5344	1.4443	-2.3924	2.4895	0.0679	3.5663	0.014	0.0331	0.0261	-0.1263	-0.1281	0.2905	-0.1813	-0.2075	0.1141	0.1144	-0.0068	0.0147	0.0827	0.0502	0.1544	-31.2415	2.0682	-11.3296
14	1.1544	-0.5826	2.3806	3.5583	-0.8116	4.9569	0.0465	-0.067	-0.3042	0.0758	0.5847	0.1561	0.1322	-0.0799	-0.6312	0.1385	-0.0649	-0.0046	0.1459	0.0128	0.0808	-27.5477	-8.3706	-13.0304
15	1.5983	0.1332	-2.2073	0.6828	-0.7427	3.5154	-0.0327	-0.1356	-0.0874	-0.042	-0.0108	0.0861	0.0784	0.177	0.0435	0.0807	-0.0014	-0.0051	0.0537	0.0104	0.0571	-18.1635	-6.9762	-6.0611
16	1.1278	-0.6212	-0.0928	3.2329	-0.4663	1.3633	-0.0731	0.0729	-0.1229	-0.0564	0.0272	0.0966	0.0743	0.0517	0.0459	0.0815	0.0028	-0.0012	0.0467	0.0117	0.0613	-15.3084	-3.6969	-17.6587
17	0.8	-0.5813	0.4418	1.7058	-0.0779	0.2906	0.0178	0.0303	0.0168	-0.0031	-0.0211	-0.0326	0.0055	0.0164	0.0033	0.0877	0.0019	-0.0009	0.0553	0.0117	0.0571	-17.5567	10.2264	-29.0061
18	0.2435	0.3262	0.7354	2.1537	1.3989	2.3217	0.0941	-0.0227	-0.0713	0.0474	0.1413	-0.2198	0.233	-0.0316	-0.2354	0.1087	-0.003	-0.0601	0.0283	-0.0061	0.0916	-23.2264	1.3746	-32.6318
19	4.3892	-3.2366	-3.8292	3.4653	1.4427	5.1086	-0.1938	-0.0334	-0.2908	0.1329	-0.0199	0.2425	0.1659	0.0793	0.2137	0.1233	-0.0283	-0.0249	0.0099	0.0053	0.0934	-28.1875	-4.0256	-26.7463
20	3.0131	2.5225	1.5674	2.1354	1.4481	2.2392	0.0495	-0.0279	0.1096	0.0113	0.0005	0.079	0.0229	-0.0586	-0.05	0.1109	-0.0164	0.003	0.0675	0.0025	0.0383	-25.2197	9.916	-15.4194
21	2.6515	1.3003	2.2124	0.7546	0.8071	2.5096	0.0093	-0.0674	0.0902	0.0095	-0.0162	0.0705	0.0029	-0.0854	0.0069	0.0815	0.0039	0.0061	0.0511	-0.0117	0.0602	-22.2427	15.9036	-20.2172
22	1.0262	0.3794	1.801	0.4284	1.1222	3.8952	0.1012	-0.0683	0.0561	-0.0227	-0.0957	-0.0367	0.1136	-0.2229	-0.0055	0.1124	-0.0185	-0.0099	0.0659	0.0083	0.04	-30.5444	5.5279	-31.4054

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 - 48
5	X-RAY DIFFRACTION	5	ALL	A	49 - 69
6	X-RAY DIFFRACTION	6	ALL	A	70 - 83
7	X-RAY DIFFRACTION	7	ALL	A	84 - 90
8	X-RAY DIFFRACTION	8	ALL	A	91 - 99
9	X-RAY DIFFRACTION	9	ALL	A	100 - 111
10	X-RAY DIFFRACTION	10	ALL	A	112 - 128
11	X-RAY DIFFRACTION	11	ALL	A	129 - 137
12	X-RAY DIFFRACTION	12	ALL	B	1 - 26
13	X-RAY DIFFRACTION	13	ALL	B	27 - 31
14	X-RAY DIFFRACTION	14	ALL	B	32 - 39
15	X-RAY DIFFRACTION	15	ALL	B	40 - 50
16	X-RAY DIFFRACTION	16	ALL	B	51 - 60
17	X-RAY DIFFRACTION	17	ALL	B	61 - 77
18	X-RAY DIFFRACTION	18	ALL	B	78 - 86
19	X-RAY DIFFRACTION	19	ALL	B	87 - 94
20	X-RAY DIFFRACTION	20	ALL	B	95 - 111
21	X-RAY DIFFRACTION	21	ALL	B	112 - 128
22	X-RAY DIFFRACTION	22	ALL	B	129 - 137

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