7D6G | pdb_00007d6g

Neutron crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+ at pH4.5

PDB DOI: https://doi.org/10.2210/pdb7D6G/pdb

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

Deposited: 2020-09-30 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: 1.65 Å
R-Value Free:
0.186 (Depositor), 0.185 (DCC)
R-Value Work:
0.157 (Depositor), 0.157 (DCC)
R-Value Observed:
0.159 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.219 (Depositor)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7D6G

This is version 1.2 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: 19.26 kDa
Atom Count: 1,464
Modeled Residue Count: 159
Deposited Residue Count: 159
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ABQ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.186 (Depositor), 0.185 (DCC)
R-Value Work: 0.157 (Depositor), 0.157 (DCC)
R-Value Observed: 0.159 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.219 (Depositor)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.102	α = 90
b = 45.595	β = 90
c = 99.113	γ = 90

Software Package:

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

Structure Validation

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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: 2024-03-27
Changes: Data collection, Database references
Version 1.2: 2024-04-03
Changes: Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.