6VDW

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Manganese(III) Porphyrin and Substrate 4-nitrophenol

PDB DOI: https://doi.org/10.2210/pdb6VDW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Amphitrite ornata
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2019-12-27 Released: 2020-12-30
Deposition Author(s): Ghiladi, R.A., de Serrano, V.S., McGuire, A., Malewschik, T.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.199
R-Value Work: 0.164
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

Currently 6VDW does not have a validation slider image.

This is version 1.1 of the entry. See complete history.

Literature

Nonnative Heme Incorporation into Multifunctional Globin Increases Peroxygenase Activity an Order and Magnitude Compared to Native Enzyme

McGuire, A.H., Petit, A.R., Kang, J., Malewschik, T., de Serrano, V., Carey, L.M., Ghiladi, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 33.39 kDa
Atom Count: 2,900
Modelled Residue Count: 274
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehaloperoxidase B	A, B	137	Amphitrite ornata	Mutation(s): 0
UniProt
Find proteins for Q9NAV7 (Amphitrite ornata) Explore Q9NAV7 Go to UniProtKB: Q9NAV7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NAV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MNR (Subject of Investigation/LOI) Query on MNR Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B]	C [auth A], M [auth B]	PROTOPORPHYRIN IX CONTAINING MN C₃₄ H₃₂ Mn N₄ O₄ UAPHVASSHGRKEN-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
NPO (Subject of Investigation/LOI) Query on NPO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B]	D [auth A], N [auth B]	P-NITROPHENOL C₆ H₅ N O₃ BTJIUGUIPKRLHP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain N [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B]	H [auth A], K [auth A], L [auth A], Q [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	R [auth B], S [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain R [auth B] Focus chain S [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	E [auth A] F [auth A] G [auth A] I [auth A] J [auth A] E [auth A], F [auth A], G [auth A], I [auth A], J [auth A], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B]