4H3D | pdb_00004h3d

1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Modified Comenic Acid.

PDB DOI: https://doi.org/10.2210/pdb4H3D/pdb

Classification: LYASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-09-13 Released: 2012-09-26
Deposition Author(s): Minasov, G., Light, S.H., Shuvalova, L., Duban, M.-E., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.199 (Depositor), 0.210 (DCC)
R-Value Work:
0.156 (Depositor), 0.160 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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: 118.12 kDa
Atom Count: 9,339
Modeled Residue Count: 1,011
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B, C, D	258	Clostridioides difficile 630	Mutation(s): 0 Gene Names: aroD, CD630_22170 EC: 4.2.1.10
UniProt
Find proteins for Q186A6 (Clostridioides difficile (strain 630)) Explore Q186A6 Go to UniProtKB: Q186A6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q186A6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SHL Query on SHL Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B], L [auth C], M [auth D]	5-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxylic acid C₇ H₆ O₅ ANRPPKUCFMTTIH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain E [auth A] mmCIF format, chain K [auth C] mmCIF format, chain E [auth A]	E [auth A], K [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain J [auth B] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain J [auth B] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain J [auth B]	J [auth B], N [auth D], O [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain J [auth B] Focus chain N [auth D] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.199 (Depositor), 0.210 (DCC)
R-Value Work: 0.156 (Depositor), 0.160 (DCC)
R-Value Observed: 0.158 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34h3d

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.275	α = 90
b = 138.688	β = 90.01
c = 66.315	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-27
Changes: Structure summary
Version 1.5: 2026-02-18
Changes: Database references