8SZD | pdb_00008szd

Crystal structure of Yersinia pestis dihydrofolate reductase at 1.25-A resolution

PDB DOI: https://doi.org/10.2210/pdb8SZD/pdb

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

Deposited: 2023-05-29 Released: 2023-06-07
Deposition Author(s): Shaw, G.X., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.221 (Depositor), 0.221 (DCC)
R-Value Work:
0.197 (Depositor), 0.197 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8SZD

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

Literature

Crystal structure of Yersinia pestis dihydrofolate reductase at 1.25-A resolution

Shaw, G.X., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.

To be published.

Macromolecule Content

Total Structure Weight: 18.59 kDa
Atom Count: 1,587
Modeled Residue Count: 161
Deposited Residue Count: 164
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	164	Yersinia pestis	Mutation(s): 0 Gene Names: folA, tmrA, YPO0486 EC: 1.5.1.3
UniProt
Find proteins for A0A3N4BLI0 (Yersinia pestis) Explore A0A3N4BLI0 Go to UniProtKB: A0A3N4BLI0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3N4BLI0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.221 (Depositor), 0.221 (DCC)
R-Value Work: 0.197 (Depositor), 0.197 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.257	α = 90
b = 79.156	β = 90
c = 64.347	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
DENZO	data reduction
AMoRE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	Intramural Research Program

Revision History (Full details and data files)

Version 1.0: 2023-06-07
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.