5E8Q | pdb_00005e8q

Crystal structure of DHFR in 20% Isopropanol

PDB DOI: https://doi.org/10.2210/pdb5E8Q/pdb

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

Deposited: 2015-10-14 Released: 2016-09-21
Deposition Author(s): Cuneo, M.J., Agarwal, P.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.253 (Depositor), 0.250 (DCC)
R-Value Work:
0.197 (Depositor), 0.190 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5UJX

Literature

Solvent conditions control enzyme dynamics and catalysis

Borrguero, J.M., Cuneo, M.J., Agarwal, P.K.

To be published.

Macromolecule Content

Total Structure Weight: 37.17 kDa
Atom Count: 3,020
Modeled 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 [auth B], B [auth A]	159	Escherichia coli	Mutation(s): 0 Gene Names: folA, AA953_06220, ABE89_23390, ABE90_01590, ABE91_11465, ABE92_27580, ABE93_03540, ABE94_26505, ABE95_19105, AC789_1c00510... folA, AA953_06220, ABE89_23390, ABE90_01590, ABE91_11465, ABE92_27580, ABE93_03540, ABE94_26505, ABE95_19105, AC789_1c00510, ACM16_01115, ACM17_00910, ACM18_00225, ACM19_01115, ACM20_00925, ACM21_22820, BN1008_2275, ECONIH1_00280, ECs0051, EL75_3711, EL79_3822, EL80_3768, HW43_03985, IY32_08385, JD73_13725, NMECO18_25965, PD07_16380, PU06_14795, PU15_01135, PU21_08285, PU33_00085, PU38_11910, PU53_21230, PU69_06270, PU71_09850, PU73_17465, RR31_00265, SK64_04362, SK65_04102, SK81_04106, SY51_00265, TZ57_00270, UC21_17710, UC41_15235, UN86_27670, UN92_06125, WQ64_08430, WQ65_17175, WQ66_04025, WQ69_03315, WQ70_09735, WQ71_08985, WQ72_04470, WQ73_14425, WQ74_13220, WQ77_00770, WQ79_09130, WQ84_04435, WQ86_16125, WQ88_00770, WQ91_15025, WQ92_19155, WQ95_08145, WQ99_15285, WR00_12370, WR01_07485, WR03_05655, WR04_00040, WR05_03890, WR12_01840, WR13_10745, WR16_15930, WR17_04125, WR18_06540, WR19_18465, WR23_10335, WR24_10640, XB00_01295, XB01_19915 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FOL Query on FOL Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain I [auth A] MOL2 format, chain C [auth B] MOL2 format, chain I [auth A] mmCIF format, chain C [auth B] mmCIF format, chain I [auth A]	C [auth B], I [auth A]	FOLIC ACID C₁₉ H₁₉ N₇ O₆ OVBPIULPVIDEAO-LBPRGKRZSA-N		Interactions Focus chain C [auth B] Focus chain I [auth A] Interactions & Density Focus chain C [auth B] Focus chain I [auth A]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain J [auth A] SDF format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth A] MOL2 format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth A] mmCIF format, chain G [auth B]	F [auth B], G [auth B], H [auth B], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth A] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.253 (Depositor), 0.250 (DCC)
R-Value Work: 0.197 (Depositor), 0.190 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.946	α = 90
b = 91.946	β = 90
c = 73.088	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-21

Deposition Author(s):

Cuneo, M.J.

Agarwal, P.K.

Revision History (Full details and data files)

Version 1.0: 2016-09-21
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description