6UXT | pdb_00006uxt

Crystal structure of unknown function protein yfdX from Shigella flexneri

PDB DOI: https://doi.org/10.2210/pdb6UXT/pdb

Classification: STRUCTURAL GENOMICS
Organism(s): Shigella flexneri 2a str. 2457T
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-11-08 Released: 2019-11-20
Deposition Author(s): Chang, C., Skarina, T., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.170 (Depositor), 0.171 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6UXT

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

Literature

Crystal structure of unknown function protein yfdX from Shigella flexneri

Chang, C., Skarina, T., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 163.03 kDa
Atom Count: 11,062
Modeled Residue Count: 1,306
Deposited Residue Count: 1,488
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YfdX protein	A, B, C, D, E A, B, C, D, E, F, G, H	186	Shigella flexneri 2a str. 2457T	Mutation(s): 0 Gene Names: yfdX,
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 L [auth F] MOL2 format, chain L [auth F] mmCIF format, chain L [auth F]	L [auth F]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain L [auth F] Interactions & Density Focus chain L [auth F]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain K [auth E] SDF format, chain I [auth B] MOL2 format, chain K [auth E] MOL2 format, chain I [auth B] mmCIF format, chain K [auth E] mmCIF format, chain I [auth B]	I [auth B], K [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain K [auth E] Interactions & Density Focus chain I [auth B] Focus chain K [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.170 (Depositor), 0.171 (DCC)
R-Value Observed: 0.172 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.579	α = 97.35
b = 92.92	β = 98.44
c = 93.469	γ = 95.46

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-11-20

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2019-11-20
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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.