7D4X

X-ray crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+ at pH7.0

PDB DOI: https://doi.org/10.2210/pdb7D4X/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-09-24 Released: 2021-06-09
Deposition Author(s): Wan, Q., Dealwis, C.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189
R-Value Work: 0.155
R-Value Observed: 0.157

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

Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis

Wan, Q., Bennett, B.C., Wymore, T., Li, Z., Wilson, M.A., Brooks III, C.L., Langan, P., Kovalevsky, A., Dealwis, C.G.

(2021) ACS Catal 11: 5873-5884

DOI: https://doi.org/10.1021/acscatal.1c00417

Macromolecule Content

Total Structure Weight: 19.21 kDa
Atom Count: 1,416
Modelled Residue Count: 159
Deposited Residue Count: 159
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	159	Escherichia coli K-12	Mutation(s): 0 Gene Names: folA, tmrA, b0048, JW0047 EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12)) Explore P0ABQ4 Go to UniProtKB: P0ABQ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABQ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FOL (Subject of Investigation/LOI) Query on FOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	FOLIC ACID C₁₉ H₁₉ N₇ O₆ OVBPIULPVIDEAO-LBPRGKRZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189
R-Value Work: 0.155
R-Value Observed: 0.157
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.293	α = 90
b = 45.625	β = 90
c = 98.974	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-06-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	32071264
National Science Foundation (NSF, China)	China	31670790

Revision History (Full details and data files)

Version 1.0: 2021-06-09
Type: Initial release
Version 1.1: 2023-11-29
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 R01GM133198.