8G50

E. coli DHFR complex with NADP+ and folate: EF-X excited state model by Laue diffraction (electric field along b axis; 8-fold extrapolation of structure factor differences)

PDB DOI: https://doi.org/10.2210/pdb8G50/pdb

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

Deposited: 2023-02-10 Released: 2024-01-03
Deposition Author(s): Greisman, J.B., Dalton, K.M., Brookner, D.E., Klureza, M.A., Hekstra, D.R.
Funding Organization(s): Searle Scholars Program, George W. Merck Fund in the New York Community Trust, National Institutes of Health/Office of the Director, National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.350
R-Value Work: 0.306
R-Value Observed: 0.309

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

E. coli DHFR complex with NADP+ and folate: EF-X excited state model by Laue diffraction (electric field along b axis; 8-fold extrapolation of structure factor differences)

Greisman, J.B., Dalton, K.M., Brookner, D.E., Klureza, M.A., Hekstra, D.R.

To be published.

Macromolecule Content

Total Structure Weight: 39.02 kDa
Atom Count: 3,127
Modelled Residue Count: 318
Deposited Residue Count: 318
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, B	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 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] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B]	D [auth A], L [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]
FOL Query on FOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B]	C [auth A], K [auth B]	FOLIC ACID C₁₉ H₁₉ N₇ O₆ OVBPIULPVIDEAO-LBPRGKRZSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.350
R-Value Work: 0.306
R-Value Observed: 0.309
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.286	α = 90
b = 45.53	β = 90
c = 98.995	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Precognition	data reduction
careless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Searle Scholars Program		SSP-2018-3240
George W. Merck Fund in the New York Community Trust		338034
National Institutes of Health/Office of the Director	United States	DP2-GM141000
National Science Foundation (NSF, United States)	United States	DGE1745303

Revision History (Full details and data files)

Version 1.0: 2024-01-03
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

8G50

E. coli DHFR complex with NADP+ and folate: EF-X excited state model by Laue diffraction (electric field along b axis; 8-fold extrapolation of structure factor differences)

E. coli DHFR complex with NADP+ and folate: EF-X excited state model by Laue diffraction (electric field along b axis; 8-fold extrapolation of structure factor differences)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)