PDB-6vd5: Crystal Structure of Dehaloperoxidase B in Complex with cofactor ...

ID or keywords:

Entry

Database: PDB / ID: 6vd5

Title

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

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: 1.64 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
Revision 1.2	Dec 25, 2024	Group: Derived calculations / Structure summary / Category: pdbx_entry_details / struct_conn / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vd5.cif.gz	173 KB	Display	PDBx/mmCIF format
PDB format	pdb6vd5.ent.gz	115.1 KB	Display	PDB format
PDBx/mmJSON format	6vd5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6vd5_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	6vd5_full_validation.pdf.gz	1.7 MB	Display
Data in XML	6vd5_validation.xml.gz	20.1 KB	Display
Data in CIF	6vd5_validation.cif.gz	25.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vd/6vd5 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/6vd5	HTTPS FTP

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Related structure data

Related structure data	6vd3C 6vd4C 6vd6C 6vdrC 6vdsC 6vdtC 6vduC 6vdvC 6vdwC 6vdxC 6vdyC 3ixfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vdu-2 6vdy-2 5exo-d 4jac-1 4flb-d 6vdy-1 6onx-1 6h64-3 6vds-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

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

1

A: Dehaloperoxidase B

hetero molecules

defined by author&software
16.7 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)	59.260, 67.996, 67.993
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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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, 178 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-T6C / 2,4,6-trichlorophenol Mass: 197.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₃Cl₃O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.22 Å³/Da / Density % sol: 44.64 %
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: Oct 26, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.64→34 Å / Num. obs: 33758 / % possible obs: 98.89 % / Redundancy: 11.6 % / B_iso Wilson estimate: 22.06 Å² / CC_1/2: 0.999 / Net I/σ(I): 40
Reflection shell	Resolution: 1.64→1.69 Å / Num. unique obs: 2243 / CC_1/2: 0.999

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Processing

Software

Name	Version	Classification
PHENIX	dev_3699	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf

Resolution: 1.64→34 Å / SU ML: 0.1629 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5503

	R_factor	Num. reflection	% reflection
R_free	0.214	1671	4.95 %
R_work	0.1795	-	-
obs	0.1811	33758	98.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 32.36 Å²

Refinement step

Cycle: LAST / Resolution: 1.64→34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2067	0	134	166	2367

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	2688
X-RAY DIFFRACTION	f_angle_d	0.8475	3705
X-RAY DIFFRACTION	f_chiral_restr	0.0561	364
X-RAY DIFFRACTION	f_plane_restr	0.004	492
X-RAY DIFFRACTION	f_dihedral_angle_d	19.0377	416

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 (%)
1.64-1.69	0.2619	131	0.2471	2544	X-RAY DIFFRACTION	95.03
1.69-1.75	0.2428	149	0.2294	2596	X-RAY DIFFRACTION	98.21
1.75-1.81	0.2869	129	0.2123	2618	X-RAY DIFFRACTION	98.85
1.81-1.88	0.2644	135	0.1957	2646	X-RAY DIFFRACTION	98.69
1.88-1.97	0.2123	159	0.1868	2620	X-RAY DIFFRACTION	98.93
1.97-2.07	0.2503	145	0.1723	2641	X-RAY DIFFRACTION	98.93
2.07-2.2	0.2049	128	0.1642	2689	X-RAY DIFFRACTION	99.33
2.2-2.37	0.207	145	0.1786	2668	X-RAY DIFFRACTION	99.54
2.37-2.61	0.235	166	0.1616	2675	X-RAY DIFFRACTION	99.72
2.61-2.98	0.1866	132	0.1723	2724	X-RAY DIFFRACTION	99.76
2.99-3.76	0.2071	109	0.1764	2784	X-RAY DIFFRACTION	99.93
3.76-34	0.1976	143	0.1799	2882	X-RAY DIFFRACTION	99.7

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	2.14222731532	0.911151089192	0.496788671433	4.2896733754	1.44838180092	2.06714736098	-0.0302873791904	-0.193456894406	0.122009418354	0.119064781789	0.0242649280501	0.297157133778	0.0439706290824	-0.13229134809	0.0202206225652	0.12963877947	-0.0064707035983	0.0130173376875	0.179456485291	0.0162179812853	0.159176632059	-15.2046798412	-7.09575894444	18.5265650296
2	3.58896733562	-3.425896941	-1.59598035603	3.32969635082	1.83596654195	2.28627586403	-0.0058569584347	0.836886772526	0.738012427863	-0.241484756731	0.280075284749	-1.11820433774	-0.441941373468	0.442843647505	-0.20220338814	0.243598481882	-0.0556021399374	0.0109885683657	0.396969821752	-0.0482675098662	0.426689364832	1.51143167134	0.995535422434	22.1319042531
3	6.26963469856	5.70768649814	-3.54013928286	5.82437602922	-3.76798590813	2.47156301017	0.292630189147	0.691424047557	0.629801960142	-1.47083323007	0.144543318398	-1.58045100775	-1.06913774071	-0.106004648487	-0.330882971784	0.683216457762	-0.0856162611678	0.110772006227	0.498601938121	0.121708179343	0.514777542184	-2.84452267776	10.093012964	18.9402918924
4	3.450099931	0.160457196778	3.00038130136	2.45857046265	1.80856993878	8.90718302209	-0.373851244541	-0.269452445493	0.395088592373	-0.0913966171731	0.119755786396	0.0367772344014	-1.00744793526	-0.540191325694	0.248443473222	0.219638077126	0.0581036643965	-0.00534283720727	0.217979832527	-0.0195938434658	0.208923808014	-12.1477085625	6.08025277104	22.9035180551
5	2.91452583108	-2.1907657506	-0.622901771399	1.69344640404	0.918275510605	3.46853982549	0.284566772379	0.126206195379	0.182733009167	-0.587098106836	-0.0516578693655	-0.259130435966	-0.463145659277	-0.220889795414	-0.214105676225	0.268417566997	-0.0325556512206	0.0348933000825	0.185415455073	0.0218919909311	0.16103669767	-12.4088366539	-8.86878851106	4.35130039132
6	4.08906367753	1.63486687272	-2.43592573457	5.41343432007	-0.967736938284	1.45133284702	0.367937103996	-0.222105676781	0.657519184542	0.76817776441	0.144083979584	0.897653764305	-0.596862479492	-0.265236350628	-0.420402522242	0.688613519822	-0.122186752637	0.443693583847	0.217887996922	0.111784873689	0.826079820172	-6.83880508277	3.51820462191	1.06887654596
7	4.97482712376	5.31927858776	-4.83131311651	5.74163041962	-5.31946102723	5.15280856039	-0.337201617622	0.591357995992	0.42959656707	-1.0820934237	0.643486060282	-0.515844765623	-0.517348900977	0.502180527424	-0.266219007853	0.454491990925	-0.128740630902	0.0601121212826	0.400591967363	-0.0905597686473	0.302320922746	0.119716011045	-3.5485214359	11.7728044366
8	7.00354692988	2.41837579894	-1.29979939447	7.61252191808	-3.23826479702	8.03543402439	0.00329728810192	-0.468621698055	-0.287004677124	0.421695015289	0.118347717766	-0.358629451726	-0.196599444472	-0.0755241718531	-0.113517591951	0.185868473096	0.0241695116835	-0.0396547349805	0.218386331391	-0.0139573005747	0.16460092619	-6.59392894861	-12.3316672482	21.5596716033
9	7.65121404442	1.96496199997	-4.57718601655	5.12717870303	-2.87334865449	8.53109647839	-0.00503534353624	-0.406924329472	-0.492489605068	-0.0953373098209	-0.0234733622019	-0.251788273672	0.144229607393	0.358496842699	0.00966311993951	0.146063541734	-0.0341811369661	-0.0236847573819	0.219294923397	-0.0137858519555	0.165511369871	-7.82475566472	-16.0747105258	14.4718444471
10	4.29204082003	0.150816185069	-1.22508339885	6.48666400158	-1.7930821882	6.56840645692	0.54056050234	-0.522100887499	0.471709644349	0.419440932928	-0.481101988378	-0.040062841452	-1.39345441133	1.52985244982	-0.0280482853055	0.560999002096	-0.148821045687	0.146590172022	0.516727334333	-0.0173253532465	0.287547318312	0.521129516683	-5.44616319384	1.92518595291
11	2.22821681509	-1.25541219871	-1.02087798083	2.8973723948	1.56379872553	4.18243050259	-0.0748369786069	-0.151728075129	0.10547653262	0.000702602027631	0.00605954855696	-0.0238872440313	-0.0685750873407	0.176814319301	0.0687323298578	0.127609829032	-0.0203516103146	0.00420426485984	0.135707892388	0.0157403808642	0.169466518302	-31.6409245142	2.1176714415	10.639356831
12	5.32158724554	0.873998970404	3.83160278955	6.52579828879	3.2333394462	4.44676381102	0.272389904093	-0.12900720777	-0.932233853208	0.824404058806	0.0152911109095	0.364255690995	0.726406466515	-1.70057399388	-0.244289646695	0.286913349112	-0.0663044105735	0.0133344674606	0.441184513118	0.0409462048155	0.358182072947	-41.622221274	3.86060919752	25.2784433249
13	9.36266134727	-4.72737580297	2.70257212505	8.55657663167	-1.14801031748	1.10518235713	-0.12398628876	-0.492774131344	0.0462196448839	0.942205824989	0.211714911037	-0.755471426414	0.149593058847	0.0774098197735	-0.093274105963	0.240452992006	0.0142652832466	-0.0980797362784	0.205085112342	-0.0571668655579	0.279592609815	-33.0464866282	11.6997357466	24.0684362603
14	8.23888614147	0.0506371981375	1.74385904136	4.45217453963	3.98042108327	4.30216635433	-0.219710544588	-0.354069119028	0.0265776670532	0.495080563395	0.187903287298	-0.445886541139	0.222612229896	0.267459098784	0.0475070715463	0.215290252222	0.0202777577129	-0.0181573634128	0.197982695698	0.00575379120064	0.209128414994	-29.3924795628	-0.745414086468	20.3277517301
15	2.51234292107	1.14891772712	2.49523453606	3.40894587328	3.0962406325	5.15655791169	0.194283409969	-0.000947138537054	-0.0299550971617	0.0870531557726	-0.138936279451	-0.23680775323	0.466557365045	-0.0241663167413	-0.0394885944033	0.230416760566	-0.00617035859038	0.0404943273433	0.128826578623	0.0185066283038	0.196194436683	-31.3463662244	-11.2659173569	6.31168493844
16	5.27863583128	-0.414167832154	-3.78048618299	1.79263147192	0.0166949155486	2.74778680655	0.982277426507	-1.36746148454	0.537800031195	1.90438440903	-0.62254432169	0.13014523648	0.0386564386128	0.445784653332	-0.279546332757	0.803840472177	-0.318203857582	0.00776596256114	0.454960969374	0.0287545776219	0.316434583684	-36.7225441607	-17.3210547527	16.081416323
17	3.2049351587	5.45163317566	4.19015078045	9.27798432326	7.12997739274	5.47877247768	0.252288865304	-1.69031434444	-1.05997344964	1.48663828659	-0.388748590924	0.183834465271	1.07486071409	-0.814796847737	-0.0268693100216	0.665681068442	-0.0797333549302	0.24343401767	0.564149649118	-0.0062295021645	0.532880609414	-45.5782625183	-8.4794113172	16.7685073706
18	9.23305736127	5.23408721895	-4.80686203617	3.09778003609	-2.6453799104	3.26584235355	-0.0804976083381	0.114038192664	0.136300043303	0.292954310135	-0.207496833495	0.219811028748	0.045518692592	-0.361398368762	0.231323566398	0.228825129203	0.0168030135413	0.0127360154557	0.182094221248	-0.0472198604657	0.240052472967	-39.9952635429	1.5445982314	7.44145937393
19	7.90104548343	3.58967357795	-2.12845525254	2.68337411568	-2.64461475806	6.51892616029	-0.078462546175	0.565723206208	0.312052166588	-0.142584998737	-0.0124510046791	0.326804351348	0.0737389265135	-0.207971596255	0.104876108077	0.174892804499	0.0158788726873	0.0377809751972	0.184800482508	-0.0225643414342	0.231791395754	-36.9448432491	-2.99856021768	0.664115261738
20	5.56149670788	1.03866771766	0.132228742599	4.30773188421	-3.5973075825	5.81813692174	0.553859849427	-0.540059428414	0.554707568479	1.29902491464	0.0351939438176	1.7055132173	-0.32168806031	-0.19662480483	-0.471206289571	0.544532047971	-0.185690118457	0.13626558328	0.302526433248	-0.00832003428753	0.461120886561	-44.9530764631	-15.1859743278	11.5397314505

Refinement TLS group

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

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