6F18

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 catodon
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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.212
R-Value Work: 0.172
R-Value Observed: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	162	Physeter catodon	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02185
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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] mmCIF 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]
EEE Query on EEE Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ETHYL ACETATE C₄ H₈ O₂ XEKOWRVHYACXOJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MHS Query on 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
R-Value Work: 0.172
R-Value Observed: 0.176
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-08-22

Deposition Author(s):

Revision History (Full details and data files)

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

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Deposit Data

Help and Resources

6F18

Structure of Mb NMH H64V, V68A mutant complex with EDA

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)