6F18 | pdb_00006f18

Structure of Mb NMH H64V, V68A mutant complex with EDA

• PDB DOI: https://doi.org/10.2210/pdb6F18/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-11-21 Released: 2018-08-22 
• Deposition Author(s): Tinzl, M., Hayashi, T., Mori, T., Hilvert, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Capture and characterization of a reactive haem-carbenoid complex in an artificial metalloenzyme

Hayashi, T., Tinzl, M., Mori, T., Krengel, U., Proppe, J., Soetbeer, J., Klose, D., Jeschke, G., Reiher, M., Hilvert, D.

(2018) Nat Catal 1

• DOI: https://doi.org/10.1038/s41929-018-0105-6

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.92 kDa 
• Atom Count: 1,432 
• Modeled Residue Count: 154 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	162	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
EEE	C [auth A]	ETHYL ACETATE C4 H8 O2 XEKOWRVHYACXOJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MHS	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.635	α = 90
b = 47.612	β = 90
c = 76.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Tinzl, M., Hayashi, T., Mori, T., Hilvert, D.

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description