7QRH | pdb_00007qrh

Crystal structure of the 5-(aminomethyl)furan-3-yl methyl phosphate kinase MfnE from Methanococcus vannielii.

PDB DOI: https://doi.org/10.2210/pdb7QRH/pdb

Classification: TRANSFERASE
Organism(s): Methanococcus vannielii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-11 Released: 2023-01-18
Deposition Author(s): Maddock, R.M.A., Race, P.R., Burton, N.M.
Funding Organization(s): UK Research and Innovation (UKRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.204 (Depositor), 0.210 (DCC)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the 5-(aminomethyl)furan-3-yl methyl phosphate kinase MfnE from Methanococcus vannielii.

Maddock, R.M.A., Race, P.R.

To be published.

Macromolecule Content

Total Structure Weight: 50.64 kDa
Atom Count: 3,272
Modeled Residue Count: 420
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate/glutamate/uridylate kinase	A [auth AAA], B [auth BBB]	228	Methanococcus vannielii	Mutation(s): 0 Gene Names: Mevan_0710
UniProt
Find proteins for A6UQ44 (Methanococcus vannielii (strain ATCC 35089 / DSM 1224 / JCM 13029 / OCM 148 / SB)) Explore A6UQ44 Go to UniProtKB: A6UQ44
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6UQ44
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth BBB] SDF format, chain C [auth AAA] MOL2 format, chain D [auth BBB] MOL2 format, chain C [auth AAA] mmCIF format, chain D [auth BBB] mmCIF format, chain C [auth AAA]	C [auth AAA], D [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth AAA] Focus chain D [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.258 (Depositor), 0.260 (DCC)
R-Value Work: 0.204 (Depositor), 0.210 (DCC)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.147	α = 90
b = 86.147	β = 90
c = 234.105	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	model building
PHASER	phasing
xia2	data scaling
xia2	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Maddock, R.M.A.

Funding Organization	Location	Grant Number
UK Research and Innovation (UKRI)	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2023-01-18
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, 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.