3WHN

Hemerythrin-like domain of DcrH I119H mutant (met)

PDB DOI: https://doi.org/10.2210/pdb3WHN/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-08-29 Released: 2014-02-26
Deposition Author(s): Okamoto, Y., Onoda, A., Sugimoto, H., Takano, Y., Hirota, S., Kurtz Jr., D.M., Shiro, Y., Hayashi, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.248
R-Value Work: 0.193
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

H2O2-dependent substrate oxidation by an engineered diiron site in a bacterial hemerythrin.

Okamoto, Y., Onoda, A., Sugimoto, H., Takano, Y., Hirota, S., Kurtz Jr., D.M., Shiro, Y., Hayashi, T.

(2014) Chem Commun (Camb) 50: 3421-3423

PubMed: 24400317 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/c3cc48108e
Primary Citation of Related Structures:
3WHN

PubMed Abstract:
The O2-binding carboxylate-bridged diiron site in DcrH-Hr was engineered in an effort to perform the H2O2-dependent oxidation of external substrates. A His residue was introduced near the diiron site in place of a conserved residue, Ile119. The I119H variant promotes the oxidation of guaiacol and 1,4-cyclohexadiene upon addition of H2O2.

Organizational Affiliation

Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan. onoda@chem.eng.osaka-u.ac.jp thayashi@chem.eng.osaka-u.ac.jp.

Macromolecule Content

Total Structure Weight: 32.77 kDa
Atom Count: 2,634
Modelled Residue Count: 266
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemerythrin-like domain protein DcrH	A, B	136	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 1 Gene Names: dcrH
UniProt
Find proteins for Q726F3 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q726F3 Go to UniProtKB: Q726F3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q726F3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CFO Query on CFO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	CHLORO DIIRON-OXO MOIETY Cl Fe₂ O KBTPJIQAZMMQJH-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.248
R-Value Work: 0.193
R-Value Observed: 0.196
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.573	α = 92.71
b = 44.082	β = 102.59
c = 46.715	γ = 90.02

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SPACE	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing