6PEY | pdb_00006pey

MTHFR with mutation Asp120Ala

PDB DOI: https://doi.org/10.2210/pdb6PEY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-06-21 Released: 2019-09-25
Deposition Author(s): Gallagher, E.L., Gurney, L.A., Frasco, F.G., Trimmer, E., Bolen, R.L., Collins, K., Garland, E., Halloran, J., Handley-Pendelton, J., Hernandez, V., Leffler, S., Perez, A., Soares, A., Stojanoff, V., Williams, D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.188 (Depositor), 0.191 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Examination of Asp120Ala a Chemically Important Novel Mutation in the Enzyme Mthylenetetrahydrofolate Reductase

Gallagher, E.L., Gurney, L.A., Frasco, F.G., Bolen, R.L., Garland, E., Halloran, J., Handley-Pendelton, J., Hernandez, V., Leffler, S., Perez, A., Soares, A., Stojanoff, V., Williams, D.

To be published.

Macromolecule Content

Total Structure Weight: 104.87 kDa
Atom Count: 6,631
Modeled Residue Count: 848
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylenetetrahydrofolate reductase	A, B, C	304	Escherichia coli	Mutation(s): 1 EC: 1.5.1.20 (PDB Primary Data), 1.5.1.54 (UniProt)
UniProt
Find proteins for P0AEZ1 (Escherichia coli (strain K12)) Explore P0AEZ1 Go to UniProtKB: P0AEZ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AEZ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.188 (Depositor), 0.191 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.747	α = 90
b = 127.744	β = 120.9
c = 95.456	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-09-25

Deposition Author(s):

Handley-Pendelton, J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM111244
Department of Energy (DOE, United States)	United States	DE-SC0012704
Department of Energy (DOE, United States)	United States	KP1605010

Revision History (Full details and data files)

Version 1.0: 2019-09-25
Type: Initial release
Version 1.1: 2019-12-04
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description