6F17 | pdb_00006f17

Structure of Mb NMH H64V, V68A mutant resting state

PDB DOI: https://doi.org/10.2210/pdb6F17/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.184 (Depositor), 0.180 (DCC)
R-Value Observed:
0.187 (Depositor)

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: 18.83 kDa
Atom Count: 1,446
Modelled Residue Count: 153
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 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02185
Sequence Annotations Expand
Reference Sequence LOADING

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] 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]

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: 1.45 Å
R-Value Free: 0.217 (Depositor), 0.220 (DCC)
R-Value Work: 0.184 (Depositor), 0.180 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.592	α = 90
b = 47.259	β = 90
c = 76.2	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, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.