4WOQ

Crystal Structures of CdNal from Clostridium difficile in complex with ketobutyric

PDB DOI: https://doi.org/10.2210/pdb4WOQ/pdb

Classification: LYASE
Organism(s): Clostridioides difficile NAP08
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-10-16 Released: 2015-10-21
Deposition Author(s): Liu, W.D., Guo, R.T., Cui, Y.F., Chen, X., Wu, Q.Q., Zhu, D.M.
Funding Organization(s): National Natural Science Foundation of China, National Basic Research Program of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.243
R-Value Work: 0.184

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystal Structures of CdNal from Clostridium difficile in complex with ketobutyric

Liu, W.D., Guo, R.T., Cui, Y.F., Chen, X., Wu, Q.Q., Zhu, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 275.77 kDa
Atom Count: 20,222
Modelled Residue Count: 2,320
Deposited Residue Count: 2,416
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylneuraminate lyase	A, B, C, D, E A, B, C, D, E, F, G, H	302	Clostridioides difficile NAP08	Mutation(s): 0 Gene Names: CdNal EC: 4.1.3.3
UniProt
Find proteins for D5Q364 (Clostridioides difficile NAP08) Explore D5Q364 Go to UniProtKB: D5Q364
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D5Q364
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2KT Query on 2KT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain O [auth G] SDF format, chain P [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth G] MOL2 format, chain P [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain O [auth G] mmCIF format, chain P [auth H]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	2-KETOBUTYRIC ACID C₄ H₆ O₃ TYEYBOSBBBHJIV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.243
R-Value Work: 0.184
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.875	α = 90
b = 122.612	β = 95.72
c = 122.186	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2015-10-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21072151
National Natural Science Foundation of China	China	21102100
National Basic Research Program of China	China	2011CB710801

Revision History (Full details and data files)

Version 1.0: 2015-10-21
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection

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4WOQ

Crystal Structures of CdNal from Clostridium difficile in complex with ketobutyric

Crystal Structures of CdNal from Clostridium difficile in complex with ketobutyric

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)