6WK3

Engineered carbene transferase RmaNOD Q52V, putative nitric oxide dioxygenase from Rhodothermus marinus

PDB DOI: https://doi.org/10.2210/pdb6WK3/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Rhodothermus marinus DSM 4252
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-04-15 Released: 2020-07-08
Deposition Author(s): Knight, A.M., Arnold, F.H.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.247
R-Value Work: 0.208
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Diversity-Oriented Enzymatic Synthesis of Cyclopropane Building Blocks.

Wittmann, B.J., Knight, A.M., Hofstra, J.L., Reisman, S.E., Kan, S.B.J., Arnold, F.H.

(2020) ACS Catal 10: 7112-7116

PubMed: 33282460 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acscatal.0c01888
Primary Citation of Related Structures:
6WK3

PubMed Abstract:
While biocatalysis is increasingly incorporated into drug development pipelines, it is less commonly used in the early stages of drug discovery. By engineering a protein to produce a chiral motif with a derivatizable functional handle, biocatalysts can be used to help generate diverse building blocks for drug discovery. Here we show the engineering of two variants of Rhodothermus marinus nitric oxide dioxygenase ( Rma NOD) to catalyze the formation of cis - and tran- diastereomers of a pinacolboronate-substituted cyclopropane which can be readily derivatized to generate diverse stereopure cyclopropane building blocks.

Organizational Affiliation

Division of Biology and Bioengineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States.

Macromolecule Content

Total Structure Weight: 68.71 kDa
Atom Count: 4,680
Modelled Residue Count: 578
Deposited Residue Count: 584
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitric oxide dioxygenase	A, B, C, D	146	Rhodothermus marinus DSM 4252	Mutation(s): 1 Gene Names: Rmar_2776 EC: 1.14.12.17
UniProt
Find proteins for D0MGT2 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10)) Explore D0MGT2 Go to UniProtKB: D0MGT2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0MGT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D]	E [auth A], H [auth B], L [auth C], P [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D]	G [auth A] J [auth B] M [auth C] O [auth C] Q [auth D] G [auth A], J [auth B], M [auth C], O [auth C], Q [auth D], R [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D]	F [auth A], I [auth B], K [auth B], N [auth C], S [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.247
R-Value Work: 0.208
R-Value Observed: 0.210
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.269	α = 90
b = 102.472	β = 98.529
c = 84.273	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Knight, A.M.

Arnold, F.H.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1513007
National Science Foundation (NSF, United States)	United States	STTR-1549855
National Science Foundation (NSF, United States)	United States	DGE-1144469
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-07616
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-112592