4X2C | pdb_00004x2c

Clostridium difficile Fic protein_0569 mutant S31A, E35A

PDB DOI: https://doi.org/10.2210/pdb4X2C/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Clostridioides difficile R20291
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2014-11-26 Released: 2015-12-23
Deposition Author(s): Jorgensen, R., Dedic, E.
Funding Organization(s): Danish Council for Independent Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (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

Structure of Clostridium difficile Fic_0569 S31A, E35A mutant at 1.8 Angstroms resolution

Jorgensen, R., Dedic, E., Alsarraf, H., Welner, D., Leeuwen, H.C., Oestergaard, O.

To be published.

Macromolecule Content

Total Structure Weight: 55.39 kDa
Atom Count: 3,736
Modeled Residue Count: 410
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fic family protein putative filamentation induced by cAMP protein	A, B	235	Clostridioides difficile R20291	Mutation(s): 2 Gene Names: CDR20291_0569
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE 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]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth B], H [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.37	α = 90
b = 67.29	β = 90
c = 139.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-12-23

Deposition Author(s):

Jorgensen, R.

Dedic, E.

Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	11-104831/FSS

Revision History (Full details and data files)

Version 1.0: 2015-12-23
Type: Initial release
Version 1.1: 2018-01-17
Changes: Author supporting evidence, Data collection
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description