5DZS | pdb_00005dzs

1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from Peptoclostridium difficile.

PDB DOI: https://doi.org/10.2210/pdb5DZS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-09-26 Released: 2015-10-07
Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.185 (Depositor), 0.190 (DCC)
R-Value Work:
0.163 (Depositor), 0.170 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile.

Rosas-Lemus, M., Dey, S., Minasov, G., Tan, K., Anderson, S.M., Brunzelle, J., Nocadello, S., Shabalin, I., Filippova, E., Halavaty, A., Kim, Y., Maltseva, N., Osipiuk, J., Minor, W., Joachimiak, A., Savchenko, A., Anderson, W.F., Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0050723-e0050723

PubMed: 37747257 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/MRA.00507-23
Primary Citation of Related Structures:
4GIB, 4H3D, 4MFG, 5DZS, 5TTA, 5TV7, 6N7M, 7K1U, 7RL8, 7RLR

PubMed Abstract:
Clostridioides difficile causes life-threatening gastrointestinal infections. It is a high-risk pathogen due to a lack of effective treatments, antimicrobial resistance, and a poorly conserved genomic core. Herein, we report 30 X-ray structures from a structure genomics pipeline spanning 13 years, representing 10.2% of the X-ray structures for this important pathogen.

Organizational Affiliation

Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Macromolecule Content

Total Structure Weight: 62.48 kDa
Atom Count: 5,100
Modeled Residue Count: 533
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate dehydrogenase (NADP(+))	A, B	276	Clostridioides difficile 630	Mutation(s): 0 Gene Names: aroE1, CD630_18370 EC: 1.1.1.25
UniProt
Find proteins for Q187E7 (Clostridioides difficile (strain 630)) Explore Q187E7 Go to UniProtKB: Q187E7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q187E7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B]	C [auth A], D [auth B], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.185 (Depositor), 0.190 (DCC)
R-Value Work: 0.163 (Depositor), 0.170 (DCC)
R-Value Observed: 0.165 (Depositor)

Diffraction Data: https://doi.org/10.18430/m35dzs

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.221	α = 77.98
b = 47.053	β = 76.44
c = 74.736	γ = 89.09

Software Package:

Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MrBUMP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-10-07

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2015-10-07
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2026-02-18
Changes: Database references, Structure summary