5ZEO

X-ray structure of sperm whale V21C/V66C/F46S myoglobin mutant with an intramolecular disulfide bond

PDB DOI: https://doi.org/10.2210/pdb5ZEO/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Physeter catodon
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-02-27 Released: 2018-05-09
Deposition Author(s): Yuan, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.266
R-Value Work: 0.223

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin

Yin, L.L., Yuan, H., Du, K.J., He, B., Gao, S.Q., Wen, G.B., Tan, X., Lin, Y.W.

(2018) Chem Commun (Camb) 54: 4356-4359

PubMed: 29645029 Search on PubMed
DOI: https://doi.org/10.1039/c8cc01646a
Primary Citation of Related Structures:
5ZEO

PubMed Abstract:
A de novo designed intramolecular disulfide bond in myoglobin, resembling that in cytoglobin without structural evidence, was confirmed by an X-ray structure for the first time and was demonstrated to regulate both the structure and function of this protein, which fulfills the design of an artificial dehaloperoxidase, with an activity exceeding that of a native enzyme.

Organizational Affiliation

School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. linlinying@hotmail.com ywlin@usc.edu.cn.

Macromolecule Content

Total Structure Weight: 17.8 kDa
Atom Count: 1,428
Modelled Residue Count: 153
Deposited Residue Count: 153
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	153	Physeter catodon	Mutation(s): 3 Gene Names: MB
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185 Go to UniProtKB: P02185
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02185
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.266
R-Value Work: 0.223
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.566	α = 90
b = 47.351	β = 90
c = 79.111	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-05-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-09
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.