PDB-6vd6: Crystal Structure of Dehaloperoxidase B in Complex with cofactor ...

ID or keywords:

Entry

Database: PDB / ID: 6vd6

Title

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

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: 1.563 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	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	6vd6.cif.gz	129.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6vd6.ent.gz	98.9 KB	Display	PDB format
PDBx/mmJSON format	6vd6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6vd6_validation.pdf.gz	511.4 KB	Display	wwPDB validaton report
Full document	6vd6_full_validation.pdf.gz	511.7 KB	Display
Data in XML	6vd6_validation.xml.gz	1.7 KB	Display
Data in CIF	6vd6_validation.cif.gz	5.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vd/6vd6 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/6vd6	HTTPS FTP

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Related structure data

Related structure data	6vd3C 6vd4C 6vd5C 6vdrC 6vdsC 6vdtC 6vduC 6vdvC 6vdwC 6vdxC 6vdyC 3ixfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6oo6-1 6vdv-1 4kmv-2 6onx-2 6onx-1 3ord-1 6oo8-1 6ch6-1 6vd3-1 6onk-1 4hsw-1 6vdy-1 6vd4-1 6vdr-1 6vdu-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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#116 - Aug 2009 Sulfotransferases 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

#116 - Aug 2009
Sulfotransferases
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
16.4 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)	59.138, 67.927, 67.867
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, 177 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-NPO / P-NITROPHENOL Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₅NO₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / 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.: 169 / 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: 2.21 Å³/Da / Density % sol: 44.36 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M Ammonium Sulphate 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: Apr 4, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.56→37.3 Å / Num. obs: 35281 / % possible obs: 94.48 % / Redundancy: 3.8 % / CC_1/2: 0.998 / Net I/σ(I): 29.4
Reflection shell	Resolution: 1.56→1.6 Å / Num. unique obs: 2132 / CC_1/2: 0.741

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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: 1.563→37.3 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.943 / SU B: 2.995 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.097
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2161	1951	5.24 %
R_work	0.1836	-	-
all	0.185	-	-
obs	-	37232	94.483 %

Solvent computation

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

Displacement parameters

B_iso mean: 18.272 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.891 Å²	0 Å²	-0 Å²
2-	-	-0.444 Å²	0 Å²
3-	-	-	-0.447 Å²

Refinement step

Cycle: LAST / Resolution: 1.563→37.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2159	0	124	169	2452

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	2627
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	2330
X-RAY DIFFRACTION	r_angle_refined_deg	2.001	1.645	3607
X-RAY DIFFRACTION	r_angle_other_deg	1.636	1.576	5473
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.962	5	343
X-RAY DIFFRACTION	r_dihedral_angle_other_1_deg	0.579	10	1
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.34	23.333	135
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	11.652	10	15
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.391	15	474
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	26.497	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	316
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3101
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	566
X-RAY DIFFRACTION	r_nbd_refined	0.252	0.2	646
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	2142
X-RAY DIFFRACTION	r_nbtor_refined	0.192	0.2	1264
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1051
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	135
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.058	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.297	0.2	31
X-RAY DIFFRACTION	r_nbd_other	0.291	0.2	73
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.135	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	0.872	1.347	1242
X-RAY DIFFRACTION	r_mcbond_other	0.871	1.347	1241
X-RAY DIFFRACTION	r_mcangle_it	1.311	2.025	1588
X-RAY DIFFRACTION	r_mcangle_other	1.311	2.026	1589
X-RAY DIFFRACTION	r_scbond_it	1.584	1.573	1385
X-RAY DIFFRACTION	r_scbond_other	1.561	1.569	1378
X-RAY DIFFRACTION	r_scangle_it	2.4	2.297	2002
X-RAY DIFFRACTION	r_scangle_other	2.371	2.289	1991
X-RAY DIFFRACTION	r_lrange_it	3.671	16.574	3207
X-RAY DIFFRACTION	r_lrange_other	3.638	16.441	3186

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 (%)
1.563-1.603	0.333	146	0.241	2132	X-RAY DIFFRACTION	78.9875
1.603-1.647	0.275	117	0.214	2426	X-RAY DIFFRACTION	90.9514
1.647-1.695	0.258	126	0.209	2469	X-RAY DIFFRACTION	95.2993
1.695-1.747	0.227	119	0.194	2479	X-RAY DIFFRACTION	98.0747
1.747-1.804	0.216	118	0.168	2379	X-RAY DIFFRACTION	97.9984
1.804-1.868	0.211	134	0.169	2309	X-RAY DIFFRACTION	98.0337
1.868-1.938	0.21	148	0.175	2192	X-RAY DIFFRACTION	97.622
1.938-2.017	0.206	129	0.165	2119	X-RAY DIFFRACTION	97.3582
2.017-2.106	0.233	100	0.17	2064	X-RAY DIFFRACTION	96.91
2.106-2.209	0.194	95	0.167	1985	X-RAY DIFFRACTION	96.8343
2.209-2.328	0.226	100	0.174	1844	X-RAY DIFFRACTION	96.4764
2.328-2.469	0.158	100	0.161	1748	X-RAY DIFFRACTION	95.0617
2.469-2.639	0.199	96	0.167	1632	X-RAY DIFFRACTION	95.8935
2.639-2.85	0.225	72	0.182	1545	X-RAY DIFFRACTION	95.2297
2.85-3.121	0.239	80	0.193	1416	X-RAY DIFFRACTION	94.8036
3.121-3.487	0.227	75	0.206	1266	X-RAY DIFFRACTION	94.0393
3.487-4.023	0.204	77	0.185	1125	X-RAY DIFFRACTION	93.9797
4.023-4.919	0.167	53	0.167	957	X-RAY DIFFRACTION	92.3218
4.919-6.92	0.242	39	0.223	766	X-RAY DIFFRACTION	92.4225
6.92-37.3	0.272	27	0.212	428	X-RAY DIFFRACTION	87.5

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	0.3019	-0.0255	-0.0347	0.3449	-0.119	0.1878	-0.0285	-0.0704	-0.002	-0.0027	0.0048	-0.0506	0.0008	0.0046	0.0237	0.0376	-0.0083	0.0032	0.0457	-0.0011	0.0333	-14.7682	7.0724	-15.3554
2	1.6725	1.0841	0.3163	3.0804	2.0747	1.5406	-0.0888	0.089	-0.087	0.0001	0.1029	-0.0116	0.0216	0.0238	-0.014	0.0095	0.0139	0.024	0.1096	0.0713	0.1043	-31.1903	-1.473	-12.4194
3	1.7491	-1.1389	2.951	9.2222	-4.8597	5.9972	0.1504	0.1167	-0.1527	-0.0959	0.1092	0.0886	0.2562	0.1297	-0.2596	0.0484	-0.0181	-0.001	0.0507	-0.0078	0.0457	-26.861	-9.8607	-15.9902
4	0.9241	0.1828	-0.5149	0.3911	-0.1928	0.9591	-0.0763	0.0065	-0.0617	-0.0122	-0.0079	-0.0266	0.0783	0.0264	0.0842	0.0532	0.0088	0.0057	0.0273	-0.0029	0.0264	-17.4249	-6.1293	-11.8206
5	0.3887	-0.3366	-0.051	0.5059	-0.3805	0.8625	0.0562	0.0301	0.0011	-0.0666	-0.0555	-0.0023	0.0313	0.0286	-0.0008	0.0409	0.0049	-0.0022	0.0519	-0.0051	0.0334	-17.1035	8.2989	-29.734
6	1.8409	-1.4871	-0.6168	2.9864	-0.3965	0.6551	0.059	0.03	-0.106	-0.2553	-0.0637	0.1709	0.0934	0.0146	0.0047	0.1265	-0.0241	-0.0598	0.0289	-0.0047	0.0458	-23.4439	-5.1814	-30.668
7	1.7196	-1.5659	-1.0034	3.7885	2.3604	1.4741	0.009	0.009	-0.0532	-0.045	0.0083	-0.0091	-0.0173	-0.007	-0.0174	0.0446	-0.0528	-0.0391	0.0752	0.0461	0.0493	-30.3925	2.0498	-22.9476
8	1.1711	0.8123	0.0192	2.3787	1.926	2.0311	-0.0128	-0.0395	0.1585	-0.0061	0.0444	0.0871	0.0058	0.0398	-0.0316	0.032	0.0031	0.0033	0.0861	0.0134	0.0402	-23.0281	11.2459	-13.6794
9	1.2234	0.2821	1.0812	1.0662	0.9192	1.5586	0.0718	-0.0847	0.0737	0.0003	-0.0325	0.0263	0.0574	-0.1006	-0.0393	0.0216	-0.0097	0.0022	0.0604	0.0004	0.0827	-21.663	15.3899	-20.2398
10	0.65	0.2264	1.0822	0.3922	1.274	4.3723	0.0902	-0.0612	-0.0377	-0.0074	-0.081	0.0073	0.0498	-0.2792	-0.0092	0.0718	-0.0201	-0.034	0.0762	0.0019	0.0171	-30.1667	4.359	-32.227
11	0.1878	-0.0067	0.1449	0.0887	-0.137	0.4728	0.003	0.0038	-0.0636	0.0003	0.025	-0.0146	-0.0274	-0.0443	-0.028	0.0326	0.0029	-0.0092	0.0409	0.0096	0.0476	2.5499	-1.8949	-23.8556
12	0.2773	-1.1213	-0.35	4.9964	0.9161	0.9948	-0.0255	0.0127	0.0096	0.0996	-0.148	-0.1871	0.0413	0.0627	0.1735	0.0291	0.0024	-0.015	0.073	-0.0126	0.0953	13.0294	-3.0864	-9.5569
13	2.0837	-2.8646	1.1681	4.5016	-0.4889	3.0161	0.0443	-0.1737	-0.2742	-0.0199	0.2036	0.3075	0.0697	-0.0699	-0.2479	0.0175	-0.032	-0.0116	0.081	0.0527	0.0825	3.2295	-10.9524	-10.161
14	1.4492	-0.0495	-0.4836	1.4005	-0.6634	1.7301	-0.0841	-0.03	-0.0223	0.0808	0.0361	-0.0315	0.0251	-0.0676	0.048	0.0292	0.0097	0.0022	0.046	0.0158	0.0355	0.4359	0.7882	-13.311
15	0.5839	0.6202	-0.4053	1.0846	-0.908	0.8184	0.0281	-0.0209	0.0489	0.0415	0.0113	0.061	-0.04	-0.0175	-0.0395	0.0475	-0.0008	0.0004	0.041	0.0091	0.0429	2.5	12.2381	-27.2515
16	0.1374	0.5819	0.6082	2.4998	2.559	2.6985	0.0297	-0.0143	0.0051	0.1502	-0.0858	-0.0325	0.0703	-0.05	0.0562	0.124	-0.0925	-0.0658	0.0849	0.0169	0.1031	8.1431	15.7834	-18.3951
17	6.1467	-2.1679	-3.4834	0.8024	1.5869	5.3782	0.1574	-0.3699	0.0894	-0.053	0.1186	-0.0543	-0.0447	0.0901	-0.276	0.0764	-0.054	-0.0331	0.0536	0.02	0.0332	13.1739	9.9764	-12.9897
18	2.4805	0.5265	1.5094	1.5618	0.9708	1.2117	0.072	0.1184	0.0032	0.0872	-0.0648	-0.0505	0.0701	0.0326	-0.0071	0.0382	-0.0035	-0.019	0.0353	0.0229	0.0667	10.4683	-1.3486	-26.8728
19	2.6984	2.477	1.3502	2.8615	1.3782	1.0149	0.005	0.1035	-0.0429	0.0316	0.038	-0.0956	0.0168	0.0517	-0.0429	0.0351	0.0011	-0.0089	0.0282	0.001	0.0427	7.2981	3.525	-32.926
20	0.4497	-0.501	0.0158	4.8974	2.1369	1.0751	0.0823	-0.0081	-0.1148	-0.0201	0.1012	-0.2573	0.0156	0.052	-0.1834	0.1005	-0.0483	-0.0493	0.0416	-0.0001	0.0748	15.7611	14.7125	-22.386

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, 177 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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About Yorodumi

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Yorodumi