5ILE | pdb_00005ile

H64A sperm whale myoglobin with a Fe-tolyl moiety

PDB DOI: https://doi.org/10.2210/pdb5ILE/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Physeter macrocephalus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-03-03 Released: 2016-09-21
Deposition Author(s): Wang, B., Thomas, L.M., Richter-Addo, G.B.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.179 (Depositor), 0.185 (DCC)
R-Value Work:
0.153 (Depositor), 0.166 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Organometallic myoglobins: Formation of Fe-carbon bonds and distal pocket effects on aryl ligand conformations.

Wang, B., Thomas, L.M., Richter-Addo, G.B.

(2016) J Inorg Biochem 164: 1-4

PubMed: 27687333 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jinorgbio.2016.06.028
Primary Citation Related Structures:
5IKS, 5ILE, 5ILM, 5ILP, 5ILR

PubMed Abstract:
Bioorganometallic Fe-C bonds are biologically relevant species that may result from the metabolism of natural or synthetic hydrazines. The molecular structures of four new sperm whale mutant myoglobin derivatives with Fe-aryl moieties, namely H64A-tolyl-m, H64A-chlorophenyl-p, H64Q-tolyl-m, and H64Q-chlorophenyl-p, have been determined at 1.7-1.9Å resolution. The structures reveal conformational preferences for the substituted aryls resulting from attachment of the aryl ligands to Fe at the site of net -NHNH ₂ release from the precursor hydrazines, and show distal pocket changes that readily accommodate these bulky ligands.

Organizational Affiliation

Department of Chemistry and Biochemistry, and Price Family Foundation Institute of Structural Biology, University of Oklahoma, Norman 73019, United States.

Macromolecule Content

Total Structure Weight: 18.58 kDa
Atom Count: 1,502
Modeled Residue Count: 154
Deposited Residue Count: 154
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	154	Physeter macrocephalus	Mutation(s): 2 Gene Names: MB EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185 Go to UniProtKB: P02185
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02185
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6CQ Query on 6CQ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	[3,3'-(7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)di(propanoato)(2-)](3-methylphenyl)iron C₄₁ H₃₉ Fe N₄ O₄ AESCELVCCZWTTN-HXFTUNQESA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.179 (Depositor), 0.185 (DCC)
R-Value Work: 0.153 (Depositor), 0.166 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.794	α = 90
b = 90.794	β = 90
c = 45.317	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	phasing
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-09-21

Deposition Author(s):

Wang, B.

Thomas, L.M.

Richter-Addo, G.B.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE 1213674

Revision History (Full details and data files)

Version 1.0: 2016-09-21
Type: Initial release
Version 1.1: 2016-10-19
Changes: Database references
Version 1.2: 2016-12-28
Changes: Database references
Version 1.3: 2017-09-27
Changes: Author supporting evidence, Refinement description
Version 1.4: 2019-11-27
Changes: Author supporting evidence
Version 1.5: 2023-09-27
Changes: Data collection, Database references, Refinement description